Crystal structure of yqeJ and uses thereof

Abstract

This invention is directed to the crystal structure of yqeJ, and to the use of this structure in rational drug design methods to identify agents that may interact with active sites of yqeJ. Such agents may be useful as antibacterial agents.

Description

FIELD OF THE INVENTION

[0002] The present invention relates to the identification of Bacillus subtilis yqeJ as a NaMN AT, the determination of the crystal structures of yqeJ alone and bound to NaAD, and the use of the structures for designing new antimicrobial agents.

BACKGROUND OF THE INVENTION

[0003] Nicotinamide adenine dinucleotide (NAD) is an essential molecule in cells. In addition to its role in oxidation-reduction reactions, in which NAD (H) and its phosphorylated form, NADP (H), act as hydride donors and acceptors, NAD is also important for other cellular processes, such as the activity of NAD-dependent DNA ligases, mono and poly ADP-ribosylation of proteins, and production of the intracellular calcium-mobilizing molecules cADPR and NaADP (1), (2).

[0004] NAD is synthesized via a multi-step de novo pathway or via a pyridine salvage pathway. The enzyme nicotinic acid mononucleotide adenylyl transferase (NaMN AT, EC 2.7.7.18) sits at the convergence of these two pathways. NaMN AT catalyzes the conversion of ATP and nicotinic acid mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD) (FIG. 1), which is directly processed to NAD by NAD synthetase. The nadD gene, encoding NaMN AT, was the first enzyme demonstrated to be essential for NAD biosynthesis by both the de novo and salvage pathways (3). A number of enzymes demonstrating in vitro adenylyltransferase activity for NaMN and NMN have been identified in eukarya, archaea and bacteria (4), (5), (6), (7), (8), (9), (10), (11). Along with sequence homology, the specificity of these enzymes for NMN versus NaMN provides a useful method for classifying new genes within this family.

[0005] While there is sequence conservation between the eubacterial nadD genes (FIG. 2), sequence alignment of nadD NaMN ATs to the eukaryotic enzymes or archeal enzymes is difficult outside of the region surrounding the (H/T)XGH nucleotidyl transferase consensus sequence. Adenylyltransferases encoded by the nadD gene prefer the nicotinic acid containing NaMN over NMN as a substrate by a factor that ranges from 6-1 to 2000-1 (12), (13), (4). Eubacteria also contain enzymes that demonstrate higher specificity for the nicotinamide containing NMN. This group the products of the nadR gene, which in addition to its regulatory role in NAD biosynthesis, also contains NMN AT activity (14). The eukaryotic and archeal NMN AT (EC 2.7.7.1), such as those from human (15), Methanococcus jannaschii (16) and Methanobacterium thermoautotrophicum (17), either demonstrate higher specificity for NMN as a substrate, as compared to NaMN, or show little preference for either substrate (4).

[0006] Primary sequence studies indicate that NaMN AT belongs to the nucleotidyl-transferase α/β phosphodiesterases superfamily of enzymes that contain the (H/T)XGH signature motif. Members of this family share the same basic catalytic mechanism, involving direct nucleophilic attack upon an α-phosphate followed by the release of pyrophosphate, while the enzyme provides stabilization of the transition state prior to the formation of a new phosphodiester bond. The recent structure determination of NMN ATs, from Methanococcus jannaschii and Methanobacterium thermoautotrophicum, has allowed this sequence and functional homology to be extended to the structural conservation of residues involved in substrate binding and catalysis (16), (17).

[0007] Genes that have been identified to be essential for bacterial survival are currently being evaluated for their potential as targets for anti-microbial chemotherapy. Understanding the biochemical, physical and structural properties of these essential enzymes and placing them in a larger biological context are the first steps in exploring this potential. The present invention is based on the identification of an unassigned reading frame in B. subtilis (yqeJ) as a NaMN AT. The recombinant enzyme was expressed in E. coli and shown to prefer NaMN as a substrate to NMN, allowing the assignment of it as the nadD gene of B. subtilis. It differs from the NMN ATs from Methanococcus jannaschii and Methanobacterium thermoautotrophicum both in its substrate specificity and oligomeric state. It is homo-dimeric as opposed to a homo-hexamer (16), (17). The three dimensional structure of NaMN AT from B. subtilis has been determined to 2.2 Å and 3.2 Å with the NaAD bound. This has allowed the identification of key residues in substrate binding and catalysis. These structures will provide invaluable information in the ongoing development of anti-microbial agents targeting NAD biosynthesis.

SUMMARY OF THE INVENTION

[0008] The present invention provides a crystallized yqeJ having four molecules of yqeJ (molecules A, B, C and D as set forth in FIG. 9) in the asymmetric unit. The present invention also provides a crystallized complex of yqeJ and NaAD, that includes six molecules of yqeJ (molecules A, B, C, D, E and F as set forth in FIG. 10) in the asymmetric unit.

[0009] The present invention also provides a three dimensional model of yqeJ as derived by x-ray diffraction data of the yqeJ crystal. Specifically, the three dimensional model of yqeJ is defined by the relative structural coordinates for molecules A, B, C and/or D of yqeJ according to FIG. 9, ±a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å. The three dimensional model of yqeJ is useful for a number of applications, including, but not limited to, the visualization, identification and characterization of various active sites of yqeJ, including the substrate binding sites of yqeJ. The active site structures may then be used to design various agents which interact with yqeJ, as well as yqeJ complexed with a substrate or related molecules.

[0010] The present invention also provides a three dimensional model of yqeJ as derived by x-ray diffraction data of the yqeJ/NaAD crystal. Specifically, the three dimensional model of yqeJ is defined by the relative structural coordinates for molecules A, B, C, D, E and/or F of yqeJ according to FIG. 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å. The three dimensional model of yqeJ is useful for a number of applications, including, but not limited to, the visualization, identification and characterization of various active sites of yqeJ, including the substrate binding sites of yqeJ. The active site structures may then be used to design various agents which interact with yqeJ, as well as yqeJ complexed with NaAD, other substrates or related molecules.

[0011] The present invention is also directed to an active site of yqeJ, and preferably the substrate binding site of yqeJ, which is most preferably NaAD. More preferably, the active site comprises the relative structural coordinates of amino acid residues Ile6, Phe7, Gly8, Gly9, Thr10, Phe11, Asp12, Pro13, Pro14, His15, Asn16, Gly17, His18, Leu19, Leu20, Met21, Ala22, Val25, Phe36, Met37, Pro38, Asn39, Glu40, Ile41, Pro42, Pro43, His44, Lys45, Tyr50, Thr51, Arg56, Glu76, Pro82, Ser83, Tyr84, Thr85, Phe86, Asp87, Thr88, Phe103, Ile104, Ile105, Gly106, Ala107, Asp108, Met109, Ile110, Tyr112, Leu113, Pro114, Lys115, Trp116, Tyr117, Lys118, Leu119, Leu122, Phe128, Ile129, Gly130, Val131, Lys132, Arg133, Pro134, Phe136, Val149, Pro150, Glu151, Phe152, Glu153, Val154, Ser155, Ser156, Thr157, Met158, Ile159, Arg160 and Tyr187 for molecules A, B, C or D of yqeJ according to FIGS. 9 or 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å. The active site may correspond to the configuration of yqeJ in its state of association with its substrate (e.g., NaAD) or in its unbound state.

[0012] In addition, the present invention provides a method for identifying an agent that interacts with yqeJ, comprising the steps of: (a) generating a three dimensional model of molecules A, B, C and/or D of yqeJ using the relative structural coordinates according to FIG. 9, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å; and (b) employing said three-dimensional model to design or select an agent that interacts with yqeJ.

[0013] The present invention also provides a method for identifying an agent that interacts with yqeJ, comprising the steps of: (a) generating a three dimensional model of molecules A, B, C, D, E and/or F of yqeJ using the relative structural coordinates according to FIG. 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å; and (b) employing said three-dimensional model to design or select an agent that interacts with yqeJ.

[0014] Still further, the present invention provides a method for identifying a potential inhibitor of yqeJ, comprising the steps of: (a) generating a three dimensional model of said molecule comprising a substrate binding site using the relative structural coordinates of amino acid residues Ile6, Phe7, Gly8, Gly9, Thr10, Phe11, Asp12, Pro13, Pro14, His15, Asn16, Gly17, His18, Leu19, Leu20, Met21, Ala22, Val25, Phe36, Met37, Pro38, Asn39, Glu40, Ile41, Pro42, Pro43, His44, Lys45, Tyr50, Thr51, Arg56, Glu76, Pro82, Ser83, Tyr84, Thr85, Phe86, Asp87, Thr88, Phe103, Ile104, Ile105, Gly106, Ala107, Asp108, Met109, Ile110, Tyr112, Leu113, Pro114, Lys115, Trp116, Tyr117, Lys118, Leu119, Leu122, Phe128, Ile129, Gly130, Val131, Lys132, Arg133, Pro134, Phe136, Val149, Pro150, Glu151, Phe152, Glu153, Val154, Ser155, Ser156, Thr157, Met158, Ile159, Arg160 and Tyr187 for molecules A, B, C or D of yqeJ according to FIGS. 9 or 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å; and (b) selecting or designing a candidate agent by performing computer fitting analysis of the candidate inhibitor with the three dimensional model generated in step (a).

[0015] Finally, the present invention provides agents or inhibitors identified using the foregoing methods. Small molecules or other agents which inhibit or otherwise interfere with substrate binding to yqeJ may be useful as antimicrobial agents.

[0016] Additional objects of the present invention will be apparent from the description which follows.

BRIEF DESCRIPTION OF THE FIGURES

[0017] FIG. 1 depicts the reaction catalyzed by yqeJ NaMN AT. NaMN AT catalyzes the reversible addition of Nicotinic Acid Mononucleotide (NaMN) or Nicotinamide Mononucleotide (NMN) to ATP yielding pyrophosphate and Nicotinic Acid Adenine Dinucleotide (NaAD) or Nicotinamide Adenine Dinucleotide (NAD), respectively.

[0018] FIG. 2 provides a sequence alignment of Bacillus subtilis yqeJ with known eubacterial nadD genes: Escherichia coli, Bacillus halodurans, Lactococcus lactis, Mycobacterium leprae, Streptomyces coelicolor, Mycobacterium tuberculosis, Treponema pallidum, Borrelia burgdorferi, Neisseria meningitidis, and Pseudomonas aeruginosa. Residues that are highlighted in bold are identical, residues that are boxed (beginning at H) designate the nucleotidyl transferase consensus sequence, while the residues in the box (beginning at S) designate the SXXXXR/K motif. The secondary structure elements of B. subtilis NaMN AT are overlaid on the sequence with the arrows and cylinders representing the β strands and α helices, respectively.

[0019] FIGS. 3A, 3B, 3C and 3D provides the results of HPLC analysis of yqeJ NaMN AT adenylyl transferase activity. 0.36 mg/ml yqeJ NaMN AT was incubated with 1 mM ATP and 1 mM NaMN (3A) or 1 mM NMN (3B) for 30 minutes. The reverse reaction with 0.18 mg/ml yqeJ NaMN AT was assayed with 1 mM sodium pyrophosphate and either 0.5 mM NaAD (3C) or 0.5 mM NAD (3D) for 30 minutes. Under these conditions NaMN eluted at 1.16 min, NMN at 1.29 min, ATP at 2.12 min, NaAD at 5.37, and NAD at 5.47 min.

[0020] FIGS. 4A-4F provide representative data of B. subtilis NaMN AT activity. Plots show rate vs. substrate concentration: (4A) NaMN, (4B) NAAD, (4C) NMN, (4D) NAD, (4E) ATP and (4F) pyrophosphate. Lines represent fit to rate equation indicated in Methods. Forward reaction, graphs 4A, 4C and 4E, uses purine ribonucleoside phosphorylase coupled assay system. Back reaction, graphs 4B, 4D and 4F, uses the hexokinase/glucose-6-phosphate dehydrogenase coupled enzyme assay system.

[0021] FIG. 5 provides a topology diagram of the secondary structure elements of yqeJ NaMN AT. Grey arrows and black cylinders represent β-sheets and α-helices, respectively. The white cylinder represents an α-helical turn and the white arrow an isolated β bridge that is part of the dimer interface.

[0022] FIGS. 6A-6F show a comparison of enzymes of the nucleotidyl-transferase α/β phosphodiesterases. 6A) B. subtilis NaMN AT, 6B) E. coli phosphopantetheine adenylyltransferase, 6C) M. jannaschii NMN AT, 6D) M. thermoautotrophicum NMN AT, 6E) B. subtilis glycerol-3-phosphate cytidyltransferase, and 6F) E. coli glytaminyl tRNA synthetase. Strands of the central parallel β-sheet, the HXGH motif and the SxxxxR/K motif are also shown.

[0023] FIGS. 7A and 7B represent ribbon diagrams of NaMN AT. A) Dimer of dimers observed in the apo crystal structure, the two ‘functional’ dimers are shown. B) The ‘functional’ dimer (lower structure from FIG. 7A) is shown bound to NaAD.

[0024] FIG. 8A is an α-carbon trace of NaMN AT monomer bound to NaAD. Inset: electron density from a 3fo-2fc composite omit map is contoured at 1σ. FIG. 8B is a schematic of selected active site interactions of NaAD with NaMN AT. MC: indicates main chain interaction, SC: indicates side chain interaction.

[0025] FIG. 9 provides the atomic structural coordinates for yqeJ NaMN AT as derived by X-ray diffraction of a yqeJ crystal. “Atom type” refers to the atom whose coordinates are being measured. “Residue” refers to the type of residue of which each measured atom is a part—i.e., amino acid, cofactor, ligand or solvent. The “x, y and z” coordinates indicate the Cartesian coordinates of each measured atom's location in the unit cell (Å). “Occ” indicates the occupancy factor. “B” indicates the “B-value”, which is a measure of how mobile the atom is in the atomic structure (Å2). Under “Residue type”, “A,” “B,” “C” and “D” refer to each molecule of yqeJ, and “S” refers to water molecules.

[0026] FIG. 10 provides the atomic structural coordinates for yqeJ NaMN AT and NaAD as derived by X-ray diffraction of the crystal complex of yqeJ NaMN AT with NaAD. “Atom type” refers to the atom whose coordinates are being measured. “Residue” refers to the type of residue of which each measured atom is a part—i.e., amino acid, cofactor, ligand or solvent. The “x, y and z” coordinates indicate the Cartesian coordinates of each measured atom's location in the unit cell (Å). “Occ” indicates the occupancy factor. “B” indicates the “B-value”, which is a measure of how mobile the atom is in the atomic structure (Å2). Under “Residue type”, “A,” “B,” “C,” “D,” “E,” and “F” refer to each molecule of yqeJ, and “H,” “J,” “K,” “L,” “M” and “N” refer to NaAD molecules.

DETAILED DESCRIPTION OF THE INVENTION

[0027] As used herein, the following terms and phrases shall have the meanings set forth below:

[0028] Unless otherwise noted, yqeJ is NaMNATase and catalyzes the reversible addition of ATP to NAMN or NMN to yield pyrophosphate and NAAD or NAD, respectively. Preferably, yqeJ comprises the amino acid sequences for Bacillus subtilis depicted in FIGS. 2, 9 or 10, including conservative substitutions. “YqeJ activity” refers to the ability of yqeJ to catalyze the aforementioned reaction.

[0029] A “substrate” is a compound or molecule involved in a reaction in which yqeJ acts as a catalyst, and binds to yqeJ. Preferably, the reaction is set forth in FIG. 1, and the substrate is NAMN, NMN and ATP, as well as the product of the reaction, namely, NaAD and NAD.

[0030] Unless otherwise indicated, “protein” or “molecule” shall include a protein, protein domain, polypeptide or peptide.

[0031] “Structural coordinates” are the Cartesian coordinates corresponding to an atom's spatial relationship to other atoms in a molecule or molecular complex. Structural coordinates may be obtained using x-ray crystallography techniques or NMR techniques, or may be derived using molecular replacement analysis or homology modeling. Various software programs allow for the graphical representation of a set of structural coordinates to obtain a three dimensional representation of a molecule or molecular complex. The structural coordinates of the present invention may be modified from the original sets provided in FIGS. 9 and 10 by mathematical manipulation, such as by inversion or integer additions or subtractions. As such, it is recognized that the structural coordinates of the present invention are relative, and are in no way specifically limited by the actual x, y, z coordinates of FIGS. 9 and 10.

[0032] An “agent” shall include a protein, polypeptide, peptide, nucleic acid (including DNA or RNA), molecule, compound or drug.

[0033] “Root mean square deviation” is the square root of the arithmetic mean of the squares of the deviations from the mean, and is a way of expressing deviation or variation from the structural coordinates described herein. The present invention includes all embodiments comprising conservative substitutions of the noted amino acid residues resulting in same structural coordinates within the stated root mean square deviation. It will be obvious to the skilled practitioner that the numbering of the amino acid residues of yqeJ may be different than that set forth herein, and may contain certain conservative amino acid substitutions that yield the same three dimensional structures as those defined by FIGS. 9 and 10 herein. Corresponding amino acids and conservative substitutions in other isoforms or analogues are easily identified by visual inspection of the relevant amino acid sequences or by using commercially available homology software programs (e.g., MODELLAR, MSI, San Diego, Calif.).

[0034] “Conservative substitutions” are those amino acid substitutions which are functionally equivalent to the substituted amino acid residue, either by way of having similar polarity, steric arrangement, or by belonging to the same class as the substituted residue (e.g., hydrophobic, acidic or basic), and includes substitutions having an inconsequential effect on the three dimensional structure of yqeJ with respect to the use of said structures for the identification and design of agents which interact with yqeJ and a substrate, as well as other proteins, peptides, molecules or molecular complexes comprising a substrate binding site, for molecular replacement analyses and/or for homology modeling.

[0035] An “active site” refers to a region of a molecule or molecular complex that, as a result of its shape and charge potential, favorably interacts or associates with another agent (including, without limitation, a protein, polypeptide, peptide, nucleic acid, including DNA or RNA, molecule, compound or drug) via various covalent and/or non-covalent binding forces. As such, an active site of the present invention may include, for example, the actual site of substrate binding with yqeJ, as well as accessory binding sites adjacent or proximal to the actual site of substrate binding that nonetheless may affect yqeJ activity upon interaction or association with a particular agent, either by direct interference with the actual site of substrate binding or by indirectly affecting the steric conformation or charge potential of the yqeJ and thereby preventing or reducing binding of substrate to yqeJ at the actual site of substrate binding. As used herein, an “active site” also includes analog residues of yqeJ, which exhibit observable NMR perturbations in the presence of a binding ligand, such as the substrate. While such residues exhibiting observable NMR perturbations may not necessarily be in direct contact with or immediately proximate to ligand binding residues, they may be critical yqeJ residues for rational drug design protocols.

[0036] The present invention first provides a crystallized yqeJ that includes four molecules of yqeJ, namely, molecules A, B, C and D, in the asymmetric unit. In a particular embodiment, the amino acid sequence of each molecule of yqeJ is set forth in FIG. 2, and includes conservative substitutions. The crystal of the present invention effectively diffracts X-rays for the determination of the structural coordinates of yqeJ, and is characterized as having space group P21, unit cell parameters of a=43.98 Å, b=126.10 Å, c=70.58 Å and β=92.73°. Each molecule of yqeJ is further characterized as having the secondary structure in which β and α strands are configured in trace order as β1, αA, β2, αB, β3, αC, β4, αD, β5, β6, αE and αF. More preferably, the β and α strands correspond to amino acid residues of each molecule of yqeJ as follows: β1 (3-9), αA (16-28), β2 (33-38), αB (53-64), β3 (70-72), αC (85-95), β4 (100-106), αD (117-125), β5 (127-132), β6 (145-148), αE (156-165) and αF (175-183).

[0037] The present invention also provides a crystallized complex of yqeJ and NaAD. The crystallized complex is preferably characterized as having space group P212121 , with unit cell parameters a=78.39 Å, b=108.90 Å, c=178.09 Å, α=β=γ=90.00° and contains six molecules of yqeJ for each molecule of NaAD in the asymmetric unit. Here again, it is preferred that the amino acid sequence of each molecule of yqeJ is set forth in FIG. 2, and includes conservative substitutions.

[0038] Using the crystals of the present invention, X-ray diffraction data can be collected by a variety of means in order to obtain the atomic coordinates of the molecules in the crystals. With the aid of specifically designed computer software, such crystallographic data can be used to generate a three dimensional structure. Various methods used to generate and refine a three dimensional structure of a molecular structure are well known to those skilled in the art, and include, without limitation, multiwavelength anomalous dispersion (MAD), multiple isomorphous replacement, reciprocal space solvent flattening, molecular replacement, and single isomorphous replacement with anomalous scattering (SIRAS).

[0039] Accordingly, the present invention also provides a three dimensional model of yqeJ as derived by x-ray diffraction data of the yqeJ crystal. The three dimensional model of yqeJ is preferably defined by the structural coordinates shown in FIG. 9 for molecules A, B, C and/or D, ± a root mean square deviation from the backbone atoms of the amino acids of not more than 1.5 Å, preferably not more than 1.0 Å, and most preferably not more than 0.5 Å. The three dimensional model may include all four molecules of yqeJ, each molecule alone, as well as combinations of the molecules (e.g., molecules A/B, A/C, A/D, B/C and B/D). The three dimensional model of yqeJ is useful for a number of applications, including, but not limited to, the visualization, identification and characterization of various active sites of yqeJ, including the substrate binding sites. The active site structures may then be used to design agents with interact with yqeJ, as well as yqeJ complexed with a substrate or related molecules.

[0040] The present invention also provides a three dimensional model of yqeJ as derived by x-ray diffraction data of the yqeJ/NaAD crystal complex. The three dimensional model of yqeJ is preferably defined by the structural coordinates shown in FIG. 10 for molecules A, B, C, D, E and/or F, ± a root mean square deviation from the backbone atoms of the amino acids of not more than 1.5 Å, preferably not more than 1.0 Å, and most preferably not more than 0.5 Å. The three dimensional model may include all six molecules of yqeJ, each molecule alone, as well as combinations of the molecules (e.g., molecules A/B, A/C, A/D, B/C and B/D, etc). However, when the model is used to define the active binding site, it is preferred that the three dimensional model is defined by the structural coordinates of the individual molecules A, B, C or D in FIG. 10 since the coordinates for these molecules are more resolved than molecules E and F. The three dimensional model of yqeJ is useful for a number of applications, including, but not limited to, the visualization, identification and characterization of various active sites of yqeJ, including the substrate binding sites. The active site structures may then be used to design agents with interact with yqeJ, as well as yqeJ complexed with NaAD, other substrates or related molecules.

[0041] The present invention is also directed to an active site of yqeJ, and preferably the substrate binding site of yqeJ. More preferably, the active site comprises the relative structural coordinates of amino acid residues Ile6, Phe7, Gly8, Gly9, Thr10, Phe11, Asp22, Pro13, Pro14, His15, Asn16, Gly17, His18, Leu19, Leu20, Met21, Ala22, Val25, Phe36, Met37, Pro38, Asn39, Glu40, Ile41, Pro42, Pro43, His44, Lys45, Tyr50, Thr51, Arg56, Glu76, Pro82, Ser83, Tyr84, Thr85, Phe86, Asp87, Thr88, Phe103, Ile104, Ile105, Gly106, Ala107, Asp108, Met109, Ile110, Tyr112, Leu113, Pro114, Lys115, Trp116, Tyr117, Lys118, Leu119, Leu122, Phe128, Ile129, Gly130, Val131, Lys132, Arg133, Pro134, Phe136, Val149, Pro150, Glu151, Phe152, Glu153, Val154, Ser155, Ser156, Thr157, Met158, Ile159, Arg160 and Tyr187 for molecules A, B, C or D of yqeJ according to FIGS. 9 or 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, preferably not more than 1.0 Å, and most preferably not more than 0.5 Å. The active site may correspond to the configuration of yqeJ in its state of association with a substrate such as NaAD, or in its unbound state.

[0042] Another aspect of the present invention is directed to a method for identifying an agent that interacts with yqeJ, comprising the steps of: (a) generating a three dimensional model of molecules A, B, C or D of yqeJ using the relative structural coordinates according to FIG. 9, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, preferably not more than 1.0 Å, and most preferably not more than 0.5 Å; and (b) employing said three-dimensional model to design or select an agent that interacts with yqeJ.

[0043] In another embodiment, the present invention is directed to a method for identifying an agent that interacts with yqeJ, comprising the steps of: (a) generating a three dimensional model of molecules A, B, C, D, E and/or F of yqeJ using the relative structural coordinates according to FIG. 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, preferably not more than 1.0 Å, and most preferably not more than 0.5 Å; and (b) employing said three-dimensional model to design or select an agent that interacts with yqeJ.

[0044] In the foregoing methods, the agent may be identified using computer fitting analyses utilizing various computer software programs that evaluate the “fit” between the putative active site and the identified agent, by (a) generating a three dimensional model of the putative active site of a molecule or molecular complex using homology modeling or the atomic structural coordinates of the active site, and (b) determining the degree of association between the putative active site and the identified agent. Three dimensional models of the putative active site may be generated using any one of a number of methods known in the art, and include, but are not limited to, homology modeling as well as computer analysis of raw data generated using crystallographic or spectroscopy data. Computer programs used to generate such three dimensional models and/or perform the necessary fitting analyses include, but are not limited to: GRID (Oxford University, Oxford, UK), MCSS (Molecular Simulations, San Diego, Calif.), AUTODOCK (Scripps Research Institute, La Jolla, Calif.), DOCK (University of California, San Francisco, Calif.), Flo99 (Thistlesoft, Morris Township, N.J.), Ludi (Molecular Simulations, San Diego, Calif.), QUANTA (Molecular Simulations, San Diego, Calif.), Insight (Molecular Simulations, San Diego, Calif.), SYBYL (TRIPOS, Inc., St. Louis. Mo.) and LEAPFROG (TRIPOS, Inc., St. Louis, Mo.). The structural coordinates also may be used to visualize the three-dimensional structure of yqeJ using MOLSCRIPT (Kraulis, P J, J. Appl. Crystallogr. 24: 946-950 (1991)) and RASTER3D (Bacon, D. J. and Anderson, W. F., J. Mol. Graph. 6: 219-220 (1998)), for example.

[0045] The effect of such an agent identified by computer fitting analyses on yqeJ activity may be further evaluated by contacting the identified agent with yqeJ and measuring the effect of the agent on yqeJ activity. Depending upon the action of the agent on the active site of yqeJ, the agent may act either as an inhibitor or activator of yqeJ activity. For example, enzymatic assays may be performed and the results analyzed to determine whether the agent is an inhibitor of yqeJ and a substrate (i.e., the agent may reduce or prevent binding affinity between yqeJ and a substrate) or an activator of yqeJ and a substrate (i.e., the agent may increase binding affinity between yqeJ and a substrate). However, in the preferred embodiment, the agent is an inhibitor of yqeJ activity. In this regard, the candidate inhibitor can be tested by obtaining the inhibitor and introducing the inhibitor in a reaction with yqeJ, NAMN (or MMN) and ATP, and determining the effect the candidate inhibitor has on the reaction. Alternatively, the candidate inhibitor can be tested by introducing the candidate inhibitor in a reaction with yqeJ, NAAD (or NAD) and pyrophosphate, and determining the effect the candidate inhibitor has on the reaction. The specific adenylyl trasferase assays that can be used are described in Example 1 below. Once a candidate inhibitor has been tested and shown to inhibit the reaction, further tests may be performed to evaluate the potential therapeutic efficacy of the agent as an antimicrobial agent.

[0046] Still further, the present invention provides a method for identifying a potential inhibitor of yqeJ, comprising the steps of: (a) generating a three dimensional model of said molecule comprising a substrate binding site using the relative structural coordinates of amino acid residues Ile6, Phe7, Gly8, Gly9, Thr10, Phe11, Asp12, Pro13, Pro14, His15, Asn16, Gly17, His18, Leu19, Leu20, Met21, Ala22, Val25, Phe36, Met37, Pro38, Asn39, Glu40, Ile41, Pro42, Pro43, His44, Lys45, Tyr50, Thr51, Arg56, Glu76, Pro82, Ser83, Tyr84, Thr85, Phe86, Asp87, Thr88, Phe103, Ile104, Ile105, Gly106, Ala107, Asp108, Met109, Ile110, Tyr112, Leu113, Pro114, Lys115, Trp116, Tyr117, Lys118, Leu119, Leu122, Phe128, Ile129, Gly130, Val131, Lys132, Arg133, Pro134, Phe136, Val149, Pro150, Glu151, Phe152, Glu153, Val154, Ser155, Ser156, Thr157, Met158, Ile159, Arg160 and Tyr187 for molecules A, B, C or D of yqeJ according to FIGS. 9 or 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å, preferably not more than 1.0 Å, and most preferably not more than 0.5 Å; and (b) selecting or designing a candidate agent by performing computer fitting analysis of the candidate inhibitor with the three dimensional model generated in step (a). Here again, once the candidate inhibitor is obtained or synthesized, the candidate inhibitor may be analyzed in various assays as discussed above.

[0047] Various molecular analysis and rational drug design techniques are further disclosed in U.S. Pat. Nos. 5,834,228, 5,939,528 and 5,865,116, as well as in PCT Application No. PCT/US98/16879, published WO 99/09148, the contents of which are hereby incorporated by reference.

[0048] The present invention is also directed to the agents or inhibitors identified using the foregoing methods. Such agents or inhibitors may be a protein, polypeptide, peptide, nucleic acid, including DNA or RNA, molecule, compound, or drug. Small molecules or other agents which inhibit or otherwise interfere with yqeJ and a substrate may be useful in the treatment of diseases or conditions associated with bacterial infection.

[0049] The present invention may be better understood by reference to the following non-limiting Example. The following Example is presented in order to more fully illustrate the preferred embodiments of the invention, and should in no way be construed as limiting the scope of the present invention.

EXAMPLE 1

[0050] 1. Methods and Methods

[0051] Cloning and Expression of B. subtilis NaMN AT.

[0052] The B. subtilis yqeJ gene was PCR cloned into a modified version of pET16b to yield pML208. This E. coli expression vector has the yqeJ coding sequence downstream of the T7 RNA polymerase promoter. The expressed protein contains the peptide MGHHHHHHHHHHSSGHIEGRHMPGGS fused to Lys-2 of the native sequence. This provides a purification tag and contains the cleavage site for Factor Xa, between Arg-20 and His-21 of the peptide, resulting in the cleaved protein having an extra six amino acids on its amino termini. To produce selenomethionine labeled yqeJ, the protein was expressed in BL21 (DE3) Escherichia coli at 25° C. Cultures were grown in shake flasks in LeMaster's media and induced at log phase with 0.5 mM IPTG. Cultures were harvested 4 hours post induction. Unlabelled yqeJ was also expressed in BL21DE3 E. coli, but at 37° C. High density expression was carried out in a Biostat C-10 bioreactor (B. Braun Biotech). The culture was induced with 1.0 mM IPTG (final) at 4.6 OD600. Cells were harvested 4 hours post induction at 9.0 OD600.

[0053] Purification and Cleavage of B. subtilis NaMN AT.

[0054] The purification, unless otherwise stated was performed at 4° C. Bacteria were resuspended in buffer (50 mM Hepes pH 7.5, 500 mM NaCl) and lysed by passage through a Microfluidics microfluidizer. The lysate was collected and centrifuged at 20,000 × g for 30 min. The supernatant, containing 40% of the expressed yqeJ NaMN AT (the remainder being insoluble), was applied to a Poros PI column (Applied Biosystems) that was coupled to a Ni-NTA column (Qiagen). The Ni-NTA column was washed with 50 mM imidazole and the protein was eluted with a 50-800 mM imidazole gradient. 10 mM EDTA was added to the fraction containing yqeJ NaMN AT, for 6 hours, followed by dialysis against 50 mM Tris pH 8.0, 50 mM NaCl, 2 mM CaCl2. The His-tag was removed from yqeJ NaMN AT by a six hour digestion with Factor Xa (New England Biolabs) at room temperature. The reaction was applied to a Poros HQ 50 column and the bound protein was eluted with a 0-1M NaCl gradient. The peak fraction containing yqeJ NaMN AT was diluted and applied to a Poros S column. The flow through, containing yqeJ NaMN AT, was applied to TSK-Gel G3000 SW column (TosoHaas), equilibrated with 50 mM Hepes pH 7.5, 50 mM NaCl. Protein purity was >95%.

[0055] Adenylyl Trasferase Assays.

[0056] Discontinuous HPLC Assay.

[0057] The discontinuous HPLC assay is based upon the assays published by Mehl et al. (12) and Balducci et al. (18). Reaction conditions were 20 mM Hepes, pH 7.4, 10 mM MgCl2, and 0.36 or 0.18 mg/ml yqeJ protein incubated at 37° C. For the forward reaction, the incubations contained 1 mM ATP and 1 mM NaMN or NMN. For the reverse reaction, the incubations contained or 1 mM sodium pyrophosphate and 0.5 mM NaAD or NAD. The reactants and products were separated by chromatography on a 3.9×150 mm C18 column (Novapack 5 μm, Waters Inc). Buffer A 100 mM potassium phosphate pH 7.5. Buffer B 100 mM potassium phosphate pH 7.5 in 20% MeOH. The elution conditions were: 0 to 3 min in 100% A, 3.0 to 3.1 min to 100% B, 3.1 to 7 min 100% B. The absorbance of reactants and products was detected at 254 nm. Under these conditions NAMN eluted at 1.16 min., NMN at 1.29 min., ATP at 2.12 min., NaAD at 5.37 min. and NAD at 5.47 min.

[0058] Continuous Assay.

[0059] A continuous assay to monitor the reaction in the forward direction was based upon the EnzChek pyrophosphate assay from Molecular Probes (Eugene Ore.) In this assay, inorganic pyrophosphate produced in the forward reaction of yqeJ is cleaved by inorganic pyrophosphatase to phosphate, which is used by the second coupling enzyme, purine nucleoside phosphorylase (PNP), to convert the chromogenic substrate 2-amino-6-mercapto-7-methylpurine ribonucleoside (MESG) to ribose-1-phosphate and 2-amino-6-mercapto-7methylpurine (E360=11,000 M−1 cm−1). The reaction conditions were 20 mM Hepes pH 7.5, 10 mM MgCl2, 0.2 mM MESG, 1 U PNP, 0.01 U inorganic pyrophosphatase, and 0.03 μg/mL yqeJ. The reaction volume was 125 μL and was carried out in a 96 well plate at room temperature using spectomax384 plus plate reader recording continuously at 360 nm (Molecular Devices, Sunnyvale Calif.). For the KM determinations, NaMN was varied from 25 to 500 μM with ATP held at 2 mM and ATP was varied from 50 to 1000 μM with NaMN held constant at 1 mM. All kinetic constants were determined from non-linear fits of the experimental data using the enzyme kinetic module of Sigmaplot 7.0 (SPSS, Inc. San Rafael Calif.). The reaction conditions were the same for the KM determinations for NMN except the MgCl2 concentration was increased to 50 mM and the yqeJ concentration was increased to 75 μg/mL due to the lower activity against this substrate. Substrate inhibition was seen in assays using NMN as a substrate, with the double reciprocal plots curving sharply upwards above 5 mM. The data was fit to a model of substrate inhibition using the equation: v=Vmax/(1+KM/S+S/Ki). The Ki determined for NMN was 17+/−3 mM. NMN was varied from 0.5 to 10 mM with ATP held constant at 0.6 mM. The kinetic constants of yqeJ using NMN and ATP substrates also was determined with a second coupled assay system, one coupling NAD production to its reduction by alcohol dehyrogenase. This assay was described by Balducci et al (Balducci et al, 1995a) and has been used to characterize other NMN ATase. Using this assay, very similar values of KM and Vmax for NMN were obtained as was determined with the PNP coupled assay described above. The alcohol dehyrogenase coupled assay was not suitable to assays NaMN as a substrate, presumably because NaAD is not a good substrate for alcohol dehydrogenase.

[0060] The back reaction for yqeJ NaMN AT was monitored using the coupled enzyme assay of hexokinase and glucose-6-phosphate dehydrogenase (from yeast). YqeJ NaMN AT converts pyrophosphate and NaAD (or NAD) to NAMN (or NMN) and ATP. The ATP is then used by hexokinase to phosphorylate glucose to give glucose-6-phosphate and ADP. Glucose-6-phosphate is oxidized to 6-phospho-glucono-δ-lactone by glucose-6-phosphate dehydrogenase and NADP is reduced to NADPH. The assay is followed by the absorbance of NADPH at 340 nm. Glucose-6-phosphate dehydrogenase from baker's yeast was used because this enzyme prefers NADP to NAD as a co-substrate. Assay conditions were: 20 mM HEPES pH 7.5, 50 mM MgCl2, 1 mM NaPPi, 10 mM KCl, 5U hexokinase, 5U glucose-6-phosphate dehydrogenase, 1 mM glucose, 0.5 mM NADP+. YqeJ concentration is 0.0015 mg/ml for NaAD determination and 0.0075 mg/ml for NAD determination. For KM determinations, NaAD was varied from 5 to 100 μM holding PPi at 1 mM, NAD was varied from 1 to 10 mM holding PPi at 1 mM and PPi was varied from 0.1 to 2 mM holding NaAD at 500 μM. At high concentration of NaPPi a precipitate was observed. This limited the concentrations of PPi that could be used in the assays.

[0061] Crystallization.

[0062] Crystals were grown by hanging drop vapor diffusion at 18° C. in drops containing 1.5 μl of protein stock solution (14 mg/ml protein, 50 mM HEPES pH 7.5, 50 mM NaCl) mixed with 1.5 μl of well solution (8% PEG 3350, 100 mM MgCl2) and equilibrated against 1 ml of well solution. Block shaped crystals grew in 3 weeks, measuring approximately 50 μm across. NaAD-NaMN AT complex co-crystals were grown at 18° C. in drops containing 1.0 μl of protein stock solution (14 mg/ml protein, 2 mM NaAD, 50 mM HEPES pH 7.5, 50 mM NaCl) mixed with 1.0 μl of well solution (20% PEG 3350, 100 mM Mg Acetate) and 0.3 μl of xylitol (30% w/v). Plate-like crystals grew in 1-3 weeks to approximately 200 μm×50 m×20 μm.

[0063] Data Collection and Processing.

[0064] Crystals of the apo-form belong to the space group P21 , with unit cell parameters a=43.98 Å, b=126.10 Å, c=70.58 Å and β=92.73° (α and γ=90°) and contain four molecules of NaMN AT in the asymmetric unit, implying a solvent content of 58.5%. To harvest crystals, an equal volume of a solution of 35% PEG 3350, 100 mM MgCl2 was added to drops, and after equilibration for several minutes crystals were swiped through another drop of this solution and cooled rapidly in liquid nitrogen. Data collection statistics are shown in Table II. MAD data were recorded at the 5.0.2 beamline of the Advanced Light Source at Lawrence Berkeley National Laboratory using a Quantum-4 detector. Data was collected at two energies chosen based on the measured absorption at the selinium K edge: 12661 eV (λ=0.97920 Å) and 12959 eV (λ=0.9567 Å) corresponding to maximum f″ and a remote energy, respectively. Intensities were integrated and scaled using the programs Denzo and Scalepack (19).

[0065] Crystals of the NaAD bound form belong to the space group P212121 with unit cell parameters a=78.39 Åb=108.90 Åc=178.09 Å, α=β=γ=90.00° and contain six molecules of yqeJ in the asymmetric unit, implying a solvent content of 55.6%. To harvest crystals, ethylene glycol was added to the drops to 20% and after mixing, the crystals were cooled rapidly in liquid nitrogen. Data collection statistics are shown in Table II. MAD data were recorded at the 5.0.2 beamline of the Advanced Light Source at Lawrence Berkeley National Laboratory using a Quantum-4 detector. Data was collected at two consecutive energies, based on the measured absorption at the selenium K edge: 12662 eV (λ=0.97910 Å) and 12863 eV (λ=0.96388 Å) and corresponding to maximum f″ and a remote energy. Intensities were integrated and scaled using the programs Denzo and Scalepack (19).

[0066] Phasing, Model Building and Refinement.

[0067] The apo structure was determined by the multiple wavelength anomalous dispersion (MAD) method. Initially 22 selenium sites were found with the program SOLVE (20), and phasing with these sites in CNS (21) revealed two additional sites by means of a difference fourier map. Phases were calculated from these 24 sites in CNS and SHARP (22) and improved by solvent modification with Solomon (22). ARP/WARP (23) was used to partially trace the α-carbon backbone. The complete model, with the exception of residues 42-52 in all molecules and residues 118-126 in molecules A and C, was built into the experimental map. After several iterative cycles of refinement using CNS and model improvement, water molecules were placed automatically in CNS. A simulated annealing composite-omit map was calculated to check the final model. Final Rwork and Rfree values of 22.21% and 25.44% were obtained.

[0068] The NaAD-NaMN AT complex structure was determined using a combination of MAD phases and molecular replacement using the apo enzyme structure. Initially 21 selenium sites found using the program ShakeNBake (24), and phasing with these sites in MLPhare (25) revealed 13 additional sites by means of a difference fourier map. Phases were calculated from these 34 sites and improved with solvent flattening and fourfold averaging with DM (25). This experimental map was used to build four of the six molecules in the asymmetric unit, employing strict NCS restraints. At this point, the refined structure of the apo-enzyme become available. The complex model was edited such that fragments of the high-resolution apo model were substituted wherever the apo model was in good agreement with electron density in the experimental map. MAD phases were then combined with model phases to generate improved maps, and two more molecules were identified. Density for the first four molecules found is significantly stronger than for the final two, however density for the bound NaAD is good in all 6 molecules. The final R values after releasing NCS restraints and rebuilding are Rfree=0.2798 and Rwork=0.2787.

[0069] Size Exclusion Chromotagraphy.

[0070] 90 μg of B. subtilis NaMN AT was run on a Pharmacia superose 12 H/R 10/30 column in Tris buffered Saline pH 7.5 at a flow rate of 0.5 ml/min. The retention time of B. subtilis NaMN AT was 27.3 min. To determine the apparent molecular weight of B. subtilis NaMN AT, the standards Thyroglobin 670,000, Gamma globulin 158,000, Ovalbumin 44,000, Myoglobin 17,000 and Vitamin B-12 1,350 (Biorad) were also run on the column under the same conditions.

[0071] Analytical Ultracentrifugation.

[0072] Protein was pre-equilibrated by dialysis at 4° C. in 20 mM HEPES and 10 mM MgCl2, pH 7.2. The partial specific volume of B. subtilis NaMN AT was calculated based on the amino acid composition, and the density of the solvent was calculated from the chemical composition of the buffer using the computer program SEDNTERP and adjusted for temperature. Sedimentation velocity experiments were performed on a Beckman XLI/XLA Analytical Ultracentrifuge operating at a rotor speed of 30,000 rpm using 400 μl samples loaded into two-channel carbon-Epon centerpieces in an An-60 Ti titanium rotor preequilibrated to temperature at least 1 hour prior to each experiment. The sedimentation coefficients and molecular weights were obtained by fitting the data to the program SVEDBERG (26). Sedimentation equilibrium experiments were performed at 4° and 20° using a rotor speed of 18,000 rpm. Samples (400 μl) were loaded into two-channel cells at 3 different protein concentrations. Scans were recorded at 4° C. and 20° C., and signal was detected using absorbance optics (280 nm) and interference optics. Equilibrium was judged to be achieved when no deviations in a plot of the difference between successive scans taken 3 hrs apart were observed, usually within 24 hours. Although, temperature and ligand did have a minor effect upon the apparent molecular weight as determined by analytical ultracentrifugation. The variation between the velocity and equilibrium values at the different protein concentrations can be attributed to hydrodynamic effects.

[0073] Equations.

[0074] The molecular weight of the protein in the presence and absence of ligand was obtained from sedimentation equilibrium experiments using the following equation:

C r =C 0 exp[m(1−{overscore (ν)}ρ)ω2(r2−r02)/2RT]+base  1)

[0075] Where Cr is absorbance at radius r; C0 is absorbance at reference radius r0; M is the molar mass of the macromolecule; ν is the partial specific volume of the macromolecule (mL/g); ρ is the density of the solvent; ω is the angular velocity of the rotor; R is gas constant; T is temperature; and base is baseline offset. The molecular weight of yqeJ NAMN AT was obtained from sedimentation velocity experiments using equation 2:

M =(sRT)/(1−{overscore (ν)}ρ)D  2)

[0076] Where s is the sedimentation coefficient and D is the diffusion coefficient obtained by fitting the data to the program SVEDBERG (26).

[0077] 2. Results

[0078] yqeJ Encodes NAMN AT nadD.

[0079] The S. pneumonia genome was sequenced and searched for essential genes that may be suitable targets for the development of anti-microbial agents. Those genes identified were then tested in B. subtilis and E. coli. An unassigned open reading frame, yqeJ that was essential in all three organisms was identified in B. subtilis. Comparisons of its amino acid sequence to genbank using the program Blast (27) revealed it has homology to a number of putative adenylyl transferases including the recently assigned nadD gene of E. coli (12). yqeJ contains the signature nucleotidyl transferase consensus sequence (H/T)XGH. As can be seen in FIG. 2, B. subtilis yqeJ is closely related to E. coli nadD and other putative eubacterial NaMN ATs. The B. subtilis enzyme is more distantly related to E. coli nadR and other eukaryotic and archeal NMN ATs. Alignment of the B. subtilis NaMN AT to these species was difficult owing to little homology outside of the region around the H/TXGH consensus sequence. This later group of enzymes includes the NMN AT from M. jannaschii and M. thermoautotrophicum for which three-dimensional structures have recently been determined (17), (16). Thus, it appears that the sequence of the B. subtilis enzyme is more closely related to the group of eubacterial enzymes that prefer NaMN as a substrate than to the archeal or eukaryotic enzymes that show little preference among the substrates or prefer NMN over NaMN (13), (12), (4). To confirm that yqeJ was indeed a NaMN AT recombinant protein was expressed in E. coli and purified (see Methods). Adenylyl transferase assays were performed to determine the activity and substrate specificity of yqeJ NaMN AT. Incubation of the enzyme with NaMN and ATP led to the formation of a new peak as detected by HPLC that eluted with the NaAD standard, the expected product of the forward reaction of NaMN AT (FIG. 3A). Similarly, the enzyme was able to convert NMN and ATP to a new peak that eluted with NAD (FIG. 3B). Using the same assay system, we were able to demonstrate that yqeJ protein was also able to catalyze the reverse reaction. FIG. 3C shows NaAD being converted to NaMN and ATP and FIG. 3D shows NAD being converted to NMN and ATP. No product was formed under any of these reaction conditions in the absence of yqeJ protein.

[0080] To better understand the substrate specificity of B. subtilis yqeJ, the catalytic constants for substrates were determined in the forward and reverse reactions using a coupled enzyme assays as described in the methods section. The data are summarized in Table I and shown in graph form in FIGS. 4A-4F. Comparing the Vmax/KM ratio for the different substrates in the forward and reverse reactions we see the B. subtilis enzyme has a clear preference for nicotinic acid containing substrates (NaMN and NaAD) over nicotinamide containing ones (NMN and NAD) by factors of 12,900 to 1 for the forward reaction and 2,000 to 1 for the reverse reaction. This same substrate preference is shared with nadD enzymes from other eubacterial sources (13), (12) and allows us to assign yqeJ as the nadD gene in B. subtilis.

[0081] The Crystal Structure of NaMN AT.

[0082] NaMN AT was crystallized both empty and with NaAD bound. For the apo structure good data were collected to 2.1 Å, while anistrophic data of the NaAD bound form were collected to 3.2 Å(Table II). The apo structure of NaMN AT was determined using experimental phases derived from selenium substituted methionine protein crystals by the MAD technique (see methods). The final model of NaMN AT contains four molecules in the asymmetric unit of which residues 42-52 are disordered in all molecules, and residues 118-126 are disordered in molecules A and C. The NaAD bound structure of NaMN AT was determined using experimental MAD phases combined with phases from molecular replacement using fragments from the apo structure. The crystal structure of NaAD bound NaMN AT contains six molecules in the asymmetric unit (two are predominantly disordered) all of which show clear density for the bound NaAD (FIG. 8A).

[0083] Subunit Structure.

[0084] NaMN AT contains 6 β-strands and 6 α-helices that form a single large domain with a smaller C-terminal lobe domain (FIG. 5). The core of the large domain is a twisted, parallel β-sheet formed by 6 β-strands (of order: 321456); a classic nucleotide-binding Rossman fold (28). Two α-helices (α-helix C and α-helix D) above and two (α-helix A and α-helix B) below the central β-sheet form characteristic right-handed β/α/β super secondary structure elements. The C-terminal lobe domain is formed by the last 33 amino acids and comprises two α-helices (E and F). Significant structural similarities place NaMN AT in the superfamily of nucleotidyl-transferase α/β phosphodiesterases (29) (FIG. 6).

[0085] The prototypical member of the nucleotidyltransferase superfamily is the class I aminoacyl-tRNA synthetase, other members include phosphopantetheine adenylyltransferase (PPAT), (29), glycerol-3-phosphate cytidylyltransferase (GCT) (30), and nicotinamide mononucleotide adenylyltransferases from M. jannaschii (NMN ATmj) (16) and M. thermoautotrophicum (NMN ATmt) (17). The RMS deviation of NaMN AT to PPAT is 2.4 Å, to NMN ATmj it is 2.9 Å, and to GCT is 3.0 Å for all Cαatoms (31). All these enzymes catalyze the same chemical reaction; the formation of a phosphodiester bond by the nucleophilic attack on the α-phosphate of ATP or CTP (for GCT) resulting in the loss of pyrophosphate and the adenylation (cytidylation) of a unique moiety (an amino acid in the case of aminoacyl-tRNA synthetases, a phosphopanteine for PPAT, glycerol-3-phosphate for GCT and a nicotinamide for the NMN ATs).

[0086] In comparison to other members of this superfamily, a striking difference of NaMN AT is the presence of a sixth strand. Since the central interactions of an important dimerization interface occur directly after β-strand 6 (see below), it is possible that the additional β-strand allows the loops following β-strand 4 and 5 the necessary flexibility to participate in substrate/product coordination. Other differences mimic the main differences between empty and NaAD bound structures of NaMN AT and center around a reordering of residues after β-strand 4 and before α-helix E. This suggests that the conformation of this region is dependent on occupation of the active site.

[0087] A Functional Dimer.

[0088] The NaAD-NaMN AT complex crystal structure reveals that NaAD binds in an extended conformation to a 20 Å long channel, almost perpendicular to the β-sheet. A large cleft at the C-terminal of β-strands 1 and 4 accommodates the di-phosphate moiety of NaAD. In the apo-NaMN AT crystal this channel is occupied, and its conformation distorted, by non-crystallographic interactions of one of the two dimers present in the asymmetric unit (FIG. 7A). This ‘handshake’ dimer buries a total surface area of 2034 Å2 per monomer with interactions that involve residues from 102 to 146 and results in the burying of an extensive hydrophobic surface and the formation of three salt-bridges. Based on the extent of the surface area and shape complementarity (Sc=0.71 (32)), and in the absence of other structural data, this dimer would likely be interpreted as being physiological relevant. It is, however, the second (‘functional’) dimer, which buries only 848 Å2 per monomer (Sc=0.64), that is seen to be conserved in the NaAD bound NaMN AT crystal (FIG. 7B). The independent crystal packing of the complex crystal structure of NaAD-NaMN AT environment presents three ‘functional’ dimers, one of which is partially disordered. The ‘functional’ dimer is formed by a pseudo-twofold symmetry operation centered around an anti-parallel β-sheet interaction from residues 151-153 (β-bridge at residue 152). In addition, the aromatic ring of Phe152 stacks with Phe152 from the other monomer and the side-chain of Glu153 interacts with its dimer equivalent backbone amide group and Pro150. An analysis of nadD sequences reveals the conservation of Pro150 and a hydrophobic residue at position 152. The ‘functional’ dimer interface is further composed of interactions of residues from a loop at the C-terminus of β-strand 5, the loop between α-helices E and F (in the lobe domain) and α-helix A. Residues which are sequentially proximal to the dimer interface form part of the ATP binding pocket (see below) suggesting a possible role for dimer formation prior to productive substrate binding.

[0089] Temperature sensitive lethal mutations in nadD from Salmonella typhimurium had also suggested a multimeric enzyme (3). The quaternary organization of B. subtilis NaMN AT was further investigated with biophysical techniques. The results of size exclusion chromatography and analytical ultracentrifugation experiments both indicate a molecular weight consistent with a dimer (Table III), a conclusion which was not affected by the addition of NaAD. These results clearly distinguished B. subtilis NaMN AT from the eight other N(a)MN ATs for which the multimeric state of the enzyme has been investigated. Two of the enzymes, from M. jannaschii (16) and M. thermoautotrophicum (17) have been shown to crystallize as homohexamers, and a third from Synechocystits was identified as a homohexamer by size exclusion chromatography (33). The remaining five, E. coli nadR (14), and the NMN ATs from S. solfataricus (11), S. cerevisiae (7), (8), Bull testes (5), and human (9, 10) appear to be trimers or tetramers by size exclusion chromatography. If the two crystal structures presented here reflect the physiological oligomeric state of NaMN AT, then the ‘functional’ dimer which is conserved in the independent crystal environments of the apo and NaAD bound form is proposed to be the dimer observed in solution. This is a surprising finding, given the large, intimate interface of the ‘handshake’ dimer. It clearly provides a caveat to the over interpretation of oligomeric states observed by crystallography and emphasizes the necessity of independent determination of quaternary structures.

[0090] NaAD Binding.

[0091] NaAD is seen bound in an extended conformation (the adenine C6 to nicotinate C2 distance is 16 Å (34)) to NaMN AT. The NaAD is buried in a large enclosed cavity (FIG. 8A) with solvent channels to the di-phosphate and nicotinic acid moieties, such that release of product would require a rearrangement of the protein. The adenylate ribose and di-phosphate moiety of NaAD bind across a groove formed by the C-terminal splitting of β-strand 1 and β-strand 4. Comparing the apo and NaAD bound NAMN AT crystal structures reveals a conformational flexibility of regions that interact with the upper binding surface of the adenylate ribose and diphosphate moiety of NaAD (FIG. 8A). However, interpretation of these conformational changes must be tempered by the extensive non-crystallographic contacts made by the formation of the handshake dimer in the apo crystal structure.

[0092] The classic alternating β strand-α helix motif of the Rossman fold unit is repeated in NaMN AT such that β-strands 4, 5 and 6 compose a modified second binding motif (FIG. 8A). It is this structural unit which is seen to have the greatest mobility upon binding of NAAD. At the C-terminal end of β-strand 4, Gly106 and Asp108 are highly conserved in nadD proteins. Gly106 interacts with the adenyl ribose ring and the side-chain of Asp108 is within hydrogen bonding distance with the guanadinium group of Arg133, another conserved residue (FIG. 8B). The aliphatic portion of the side-chain of Arg133 stacks on top of the adenine ring in a similar position to Arg260 of glutaminyl-tRNA (35) and also Arg113 of GCT. The positive charge of these conserved arginines are positioned to play a role in stabilizing the β-phosphate of the tri-phosphate substrates (36). However, Met118 and Leu124 in NMN ATmj and NMN ATmt, respectively, replace the hydrophobic stacking on the adenine ring but are positioned 3 amino acids before a conserved arginine (Arg121 and Arg127 respectively), which retains the proposed charge-charge interaction to the ATP.

[0093] More striking differences between NaMN AT and the NMN AT structures are present in the loop following β-strand 4. The NaAD bound structure of NaMN AT has a small α-helical turn prior to α-helix D. The α-helical turn starts after Asp108 and finishes before Trp116, both of which are conserved in nadD proteins (FIG. 2). The indole ring of Trp116, stacks in a parallel fashion against the lower (i.e. class B hydride transfer) surface of the pyridinic ring. A similar interaction of the pyridinic ring is seen in complexes of NMN ATmt (17). Here the bound NAD and NMN π-stack with the indole ring of Trp87, positioned on α-helix C. In NaMN AT, the dipole moment of α-helix C is positioned to complement the negative charge on the nicotinic acid. Because these critical tryptophan residues occur in different parts of the structure, the NaAD in NaMN AT has considerable conformational variation (centered mainly on the βN and γN torsion angles (IUPAC convention for NAD)) from the NMN and NAD bound to NMN ATmt. The most significant interactions that enable specificity for NaMN are the positioning of the nicotinic acid oxygens within hydrogen bonding distance to the backbone amides of Tyr117 and Thr85. The only other deamido-NAD bound protein structure available is that of NH3-dependent NAD+ synthetase from Bacillus subtilis (37), where the nicotinic group is disordered.

[0094] The loop from β-strand 2 to α-helix B becomes ordered by its interactions with NaAD. This loop contains a partially conserved P42P43H44K45 motif that interacts with both the nicotinic ring, through Pro43 and His44, and the modeled γ-phosphate of ATP through His44 and Lys45. Residues that form the floor of this pocket remain invariant in the apo and NaAD bound structures. These include Gly9, Thr10 and Phe11, at the end of β-strand 1 that interact with the di-phosphate group. The main chain oxygens of Phe152 and Ile154, immobilized at the dimerization interface, are directed towards the adenine ring. The aromatic ring of Phe7 fixes the orientation of imidazole group of His18 in an edge-on interaction. The adenine then rests on a platform comprising His15, His18, and Gly17 of the HXGH signature motif on one face and with Arg133 layered on the other.

[0095] Conserved Motifs in the Nucleotidyl-Transferase α/β Phosphodiesterases.

[0096] The signature sequence motif HXGH, first seen in class I aminoacyl-tRNA synthetases has been identified as being conserved in all nucleotidyl-transferase α/β phosphodiesterases (17). In B. subtilis NaMN AT this conserved motif is H15N16G17H18. The apo crystal structure of NaMN AT shows this loop to be unchanged in its conformation to that of NaAD bound. The two imidazole rings of His15 and His18 stack on each other in a parallel (π-π) fashion and the backbone amide of His15 hydrogen bonds to the hydroxyl of His18. The arrangement of this loop results in a similar conformation seen in all other adenylyl transferase structures. The side-chain of His18 makes extensive interactions with the adenyl ribose and the side-chain of His15 is positioned to interact with the modeled β-phosphate of ATP. Site-directed mutagenesis studies of NMN ATmt and other adenylyl transferases have implicated His15 in the loss of enzymatic activity and in the stabilization of the transition state (17).

[0097] In addition to the HXGH motif, class I aminoacyl-tRNA synthetases are characterized by a KMSKS region. The core functionality of this region can now be extended to the whole super-family by the observation that the serine stabilizes a loop at the N-terminal end of an α-helix proximal to the ATP's phosphate binding site for all known members. In NaMN AT, the tri-phosphate of ATP would be stabilized by the N-terminal dipole of α-helix E. It has been previously noted that this second conserved sequence motif seen in tRNA synthetases (K230FGKT in tyrosyl- and V267MSKR in glutaminyl-tRNA synthetase) has a structurally equivalent R113TXGISTT motif in the GCT family (30). Both these sequences lie at the N-terminal end of an α-helix and make direct interactions to the β- and γ-phosphates of bound ATP. Comparison of the current complex structure with the two published NMN AT structures shows a similar set of structural interactions from conservatively mutated sequences and suggests an equivalent sequence motif (FIG. 6). The key residues of this motif for cytidylyl transferase and adenylyltransferases appear to be the initial serine and the terminal arginine/lysine and suggest a SnxxxxR/Kn+5 minimal consensus sequence (Table IV). The main chain carbonyl preceding the seminal serine is within hydrogen-bonding distance to the exocyclic nitrogen of adenine and the Oγ of this serine (at position n) is within hydrogen-bonding distance to the n+3 main-chain nitrogen. This appears to cap the N-terminal of an α-helix whose dipole moment stabilizes the tri-phosphate binding pocket. Further, this α-helix is not part of the β/α/β dinucleotide binding fold, but occurs in a distinct domain. The positive charge at position n+5 of this motif appears to coordinate the γ-phosphate of ATP in NMN ATmj, consistent with modeling studies for Arg160 of NaMN AT. In GCT, however, Lys123 is built pointing away from the catalytic active site, but the higher temperature factor for the side chain may indicate a high degree mobility. In pantothenate synthetase (PS), this motif occurs in a region that is believed to show dramatic structural rearrangment (37). The crystal structure of glutaminyl-tRNA synthetase complexed with tRNA and ATP shows that the positively charged residue is on the same face of the α-helix, but positioned only a half-turn from the seminal serine. Further studies should reveal whether the composition of this α-helix plays a role in catalysis.

[0098] While these residues are structurally conserved among known structures in this superfamily, other contributors to the active site vary. An arginine from β-strand 1 in NMN ATmj and NMN ATmt (Arg8 and Arg11, respectively) contributes to stabilization of the tri-phosphate group of ATP. In contrast PPAT, GCT and NaMN AT lack this residue, but the conserved Lys42 in PPAT (Lys46 of GCT and Lys45 of NaMN AT) is thought to play a similar role.

[0099] In conclusion, the B. subtilis yqeJ gene encoding NaMN AT has been identified as an essential part of the NAD synthesis pathway exhibiting structural homology to other known adenylyltransferases. The biochemical and structural characterization of substrate specificity (NaMN vs NMN) may provide an exciting new target for anti-microbial therapies. Further studies are needed to elucidate the function of NaMN AT dimerization and the role of the conserved sequence and structural motifs in catalysis.

TABLE I
Kinetic constants for NaMN AT
Substrate	KM (mM)	Vmax (μmol/min/mg)	Vmax/KM
NaMNa	0.043 +/− 0.009	11.1 +/− 0.7	258
NMNa,b	2.3 +/− 0.2	0.054 +/− 0.003	0.02
ATPa,c	0.135 +/− 0.013	10.1 +/− 0.4
NAADd,e	0.0068 +/− 0.0012	2.8 +/− 0.2	412
NADd,e	1.7 +/− 0.2	0.34 +/− 0.01	0.2
PPid,f	4.2 +/− 0.6	11.5 +/− 1.3
akinetic constants for forward reaction.
bData for NMN was fit to the equation for substrate inhibition: v = Vmax/(1 + KM/S + S/Ki); Ki NMN = 17 +/− 3 mM.
cat saturating concentrations of NaMN.
dkinetic constants for back reaction.
eat subsaturating concentrations of PPi.
fat saturating concentrations of NaAD.

[0100]

TABLE II
Statistics for Data Collection, Phase Determination, and Refinement
Data Collection	peak	remote
empty yqeJ
wavelength (Å)	0.9792	0.9567
resolution range (Å)	20-2.2	20-2.0
Rmergea (%)	10.3 (45.3)	7.9 (47.0)
completeness (%)	100.0 (100.0)	99.9 (99.8)
total reflections	286583	196259
unique reflections	38710	51680
I/σ(I)	22.7 (3.3)	16.4 (2.4)
NAAD bound yqeJ
wavelength (Å)	0.9791	0.9639
resolution range (Å)	15.0-3.2	15.0-3.4
Rmergea (%)	14.7 (28.9)	11.1 (27.6)
completeness (%)	96.5 (84.0)	96.8 (79.0)
total reflections	80499	99889
unique reflections	24599	20850
I/σ(I)	16.0 (5.6)	12.3 (4.8)
Model Refinement	NaMN AT	NAAD-NaMN AT
maximum resolution (Å)	2.1	3.2
Rworkb (%)	22.21	27.87
Rfree (%)	25.44	27.98
RMS deviations from
ideal geometry for:
bonds (Å)	0.009	0.012
angles (°)	1.347	1.913
non-hydrogen protein atom	7848	9051
water molecules	139	0
a Rmerge = |Ih − <Ih>|/Ih, where <Ih> is the average intensity over symmetry equivalents. Numbers in parentheses reflect statistics for the last shell.
b Rwork = | |Fobs| − |Fcalc| |/|Fobs|
c Rfree is equivalent to Rwork, but calculated for a randomly chosen 5% of reflections omitted from the refinement process.

[0101]

TABLE III
Apparent Molecular Weights of NaMN AT
Conditions	Method	Temp.	MW, app
79 μMa	SECb	20° C.	42758
44 μM	equilibriumc	20° C.	47622 ± 224
44 μM	velocity	20° C.	41200
22 μM	equilibrium	20° C.	48182 ± 467
22 μM	velocity	20° C.	43400
4.4 μM	equilibrium	20° C.	49138 ± 570
16 μM	equilibrium	4° C.	42502 ± 209
16 μM	velocity	4° C.	41500
133 μM + 1 mM NAAD	equilibrium	4° C.	36370 ± 221
16 μM + 1 mM NAAD	equilibrium	4° C.	39545 ± 169
a concentration based on monomer molecular weight
b size exclusion chromatography
c Results obtained from a fit of the data to a single ideal species model

[0102]

TABLE IV
SXXXXR/K motif in cytidylyl transferase and adenylyl
transferase families
B. subtilis NaMN AT	S155	S156	T157	M158	I159	R160
NMN ATmj	S125	G126	T127	E128	I129	R130
NMN ATmt	S131	G132	T133	E134	V135	R136
PPAT	S128	S129	S130	L131	V132	K133
GCT	S118	T119	T120	K121	I122	K123
glutaminyl -tRNA synth.	S269	K270	—	—	—	R271
PS	S187	S188	—	—	—	R189
consensus	S	X	X	X	X	R/K

[0103]

TABLE V
Residues from YQEJ which are within 8 Å of NaAD and modeled
phosphates of ATP.
Ile6, Phe7, Gly8, Gly9, Thr10, Phe11, Asp12, Pro13, Pro14, His15,
Asn16, Gly17, His18, Leu19, Leu20, Met21, Ala22, Val25, Phe36,
Met37, Pro38, Asn39, Glu40, Ile41, Pro42, Pro43, His44, Lys45, Tyr50,
Thr51, Arg56, Glu76, Pro82, Ser83, Tyr84, Thr85, Phe86, Asp87, Thr88,
Phe103, Ile104, Ile105, Gly106, Ala107, Asp108, Met109, Ile110,
Tyr112, Leu113, Pro114, Lys115, Trp116, Tyr117, Lys118, Leu119,
Leu122, Phe128, Ile129, Gly130, Val131, Lys132, Arg133, Pro134,
Phe136, Val149, Pro150, Glu151, Phe152, Glu153, Val154, Ser155,
Ser156, Thr157, Met158, Ile159, Arg160, Tyr187

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[0142] All publications mentioned herein above, whether to issued patents, pending applications, published articles, or otherwise, are hereby incorporated by reference in their entirety. While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be appreciated by one skilled in the art from a reading of the disclosure that various changes in form and detail can be made without departing from the true scope of the invention in the appended claims.

Claims

1. A crystallized yqeJ having four molecules of yqeJ in the asymmetric unit.

2. The crystallized yqeJ of claim 1, characterized as having space group P21, unit cell parameters of a=43.98 Å, b=126.10 Å, c=70.58 Å and β=92.73°.

3. The crystallized yqeJ of claim 1, wherein each molecule of yqeJ is characterized as having the secondary structure in which β and α strands are configured in trace order as β1, αA, β2, αB, β3, αC, β4, αD, β5, β6, αE and αF.

4. The crystallized yqeJ of claim 3, wherein the β and α strands correspond to amino acid residues of each molecule of yqeJ as follows: β1 (3-9), αA (16-28), β2 (33-38), αB (53-64), β3 (70-72), αC (85-95), β4 (100-106), αD (117-125), β5 (127-132), β6 (145-148), αE (156-165) and αF (175-183).

5. The crystallized yqeJ of claim 1, having a three dimensional structure defined by the relative structural coordinates for molecules A, B, C and D of yqeJ according to FIG. 9, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å.

6. The crystallized yqeJ of claim 5, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 1.0 Å.

7. The crystallized yqeJ of claim 5, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 0.5 Å.

8. A crystallized complex of yqeJ and NaAD.

9. The crystallized complex of claim 8, characterized as having space group P212121 with unit cell parameters a=78.39 Å, b=108.90 Å, c=178.09 Å, α=β=γ=90.00°.

10. The crystallized complex of claim 8, containing six molecules of yqeJ in the asymmetric unit.

11. A three dimensional model of yqeJ defined by the relative structural coordinates for molecules A, B, C and/or D of yqeJ according to FIG. 9, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å.

12. The three dimensional model of claim 11, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 1.0 Å.

13. The three dimensional model of claim 11, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 0.5 Å.

14. A three dimensional model of yqeJ defined by the relative structural coordinates for molecules A, B, C, D, E and/or F of yqeJ according to FIG. 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å.

15. The three dimensional model of claim 13, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 1.0 Å.

16. The three dimensional model of claim 13, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 0.5 Å.

17. An active site of yqeJ, wherein said active site comprises the relative structural coordinates of amino acid residues Ile6, Phe7, Gly8, Gly9, Thr10, Phe11, Asp12, Pro13, Pro14, His15, Asn16, Gly17, His18, Leu19, Leu20, Met21, Ala22, Val25, Phe36, Met37, Pro38, Asn39, Glu40, Ile41, Pro42, Pro43, His44, Lys45, Tyr50, Thr51, Arg56, Glu76, Pro82, Ser83, Tyr84, Thr85, Phe86, Asp87, Thr88, Phe103, Ile104, Ile105, Gly106, Ala107, Asp108, Met109, Ile110, Tyr112, Leu113, Pro114, Lys115, Trp116, Tyr117, Lys118, Leu119, Leu122, Phe128, Ile129, Gly130, Val131, Lys132, Arg133, Pro134, Phe136, Val149, Pro150, Glu151, Phe152, Glu153, Val154, Ser155, Ser156, Thr157, Met158, Ile159, Arg160 and Tyr187 for molecules A, B, C or D of yqeJ according to FIGS. 9 or 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å.

18. The active site of claim 17, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 1.0 Å.

19. The active site of claim 17, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 0.5 Å.

20. A method for identifying an agent that interacts with yqeJ, comprising the steps of: (a) generating a three dimensional model of molecules A, B, C and/or D of yqeJ using the relative structural coordinates according to FIG. 9, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å; and (b) employing said three-dimensional model to design or select an agent that interacts with yqeJ.

21. The method of claim 20, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 1.0 Å.

22. The method of claim 20, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 0.5 Å.

23. The method of claim 20, further comprising the steps of: (c) obtaining the identified agent; and (d) contacting the identified agent with yqeJ in order to determine the effect the agent has on yqeJ activity.

24. A method for identifying an agent that interacts with yqeJ, comprising the steps of: (a) generating a three dimensional model of molecules A, B, C, D, E and/or F of yqeJ using the relative structural coordinates according to FIG. 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å; and (b) employing said three-dimensional model to design or select an agent that interacts with yqeJ.

25. The method of claim 24, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 1.0 Å.

26. The method of claim 24, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 0.5 Å.

27. The method of claim 24, further comprising the steps of: (c) obtaining the identified agent; and (d) contacting the identified agent with yqeJ in order to determine the effect the agent has on yqeJ activity.

28. A method for identifying a potential inhibitor of yqeJ, comprising the steps of: (a) generating a three dimensional model of yqeJ using the relative structural coordinates of amino acid residues Ile6, Phe7, Gly8, Gly9, Thr10, Phe11, Asp12, Pro13, Pro14, His15, Asn16, Gly17, His18, Leu19, Leu20, Met21, Ala22, Val25, Phe36, Met37, Pro38, Asn39, Glu40, Ile41, Pro42, Pro43, His44, Lys45, Tyr50, Thr51, Arg56, Glu76, Pro82, Ser83, Tyr84, Thr85, Phe86, Asp87, Thr88, Phe103, Ile104, Ile105, Gly106, Ala107, Asp108, Met109, Ile110, Tyr112, Leu113, Pro114, Lys115, Trp116, Tyr117, Lys118, Leu119, Leu122, Phe128, Ile129, Gly130, Val131, Lys132, Arg133, Pro134, Phe136, Val149, Pro150, Glu151, Phe152, Glu153, Val154, Ser155, Ser156, Thr157, Met158, Ile159, Arg160 and Tyr187 for molecules A, B, C or D of yqeJ according to FIGS. 9 or 10, ± a root mean square deviation from the backbone atoms of said amino acids of not more than 1.5 Å; and (b) selecting or designing a candidate agent by performing computer fitting analysis of the candidate inhibitor with the three dimensional model generated in step (a).

29. The method of claim 28, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 1.0 Å.

30. The method of claim 28, wherein the ± a root mean square deviation from the backbone atoms of said amino acids is not more than 0.5 Å.

31. The method of claim 28, which further comprises the steps of: (c) obtaining the candidate inhibitor; (d) introducing the candidate inhibitor in a reaction with yqeJ, NAMN (or MMN) and ATP; and (e) determining the effect the candidate inhibitor has on the reaction.

32. The method of claim 28, which further comprises the steps of: (c) obtaining the candidate inhibitor; (d) introducing the candidate inhibitor in a reaction with yqeJ, NAAD (or NAD) and pyrophosphate; and (e) determining the effect the candidate inhibitor has on the reaction.

33. An agent identified by the method of claim 20.

34. An agent identified by the method of claim 24.

35. An inhibitor identified by the method of claim 28.