Structure of MurF from Streptococcus pneumoniae co-crystallized with a small molecule inhibitor exhibits interdomain closure

Protein Science

Volumn 14, Issue 12, 2005, Pages 3039-3047

  Longenecker, Kenton L ^a,b   Stamper, Geoffrey F ^a   Hajduk, Philip J ^a   Fry, Elizabeth H ^a   Jakob, Clarissa G ^a   Harlan, John E ^a   Edalji, Rohinton ^a   Bartley, Diane M ^a   Walter, Karl A ^a   Solomon, Larry R ^a   Holzman, Thomas F ^a   Yu, Gui Gu ^a   Lerner, Claude G ^a   Beutel, Bruce A ^a   Stoll, Vincent S ^a  

^a ABBOTT LABORATORIES   (United States)

^b Building AP10 ^*  (United States)

Author keywords

Multidomain structure; Murein enzymes; MurF; NMR; Peptidoglycan; Protein ligand interaction; X ray

Indexed keywords

BACTERIAL PROTEIN; GENE PRODUCT; PROTEIN MURF; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATION; CONTROLLED STUDY; CRYSTALLIZATION; GENOMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; STREPTOCOCCUS PNEUMONIAE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE SYNTHASES; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STREPTOCOCCUS PNEUMONIAE; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); MAMMALIA; STREPTOCOCCUS; STREPTOCOCCUS PNEUMONIAE;

EID: 28844504713     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.051604805     Document Type: Article

References (23)

1. Anderson, M.S., Eveland, S.S., Onishi, H.R., and Pompliano, D.L. 1996. Kinetic mechanism of the Escherichia coli UDPMurNAc-tripeptide Dalanyl-D-alanine-adding enzyme: Use of a glutathione S-transferase fusion. Biochemistry 35: 16264-16269.
2. Bertrand, J.A., Auger, G., Martin, L., Fanchon, E., Blanot, D., Le Beller, D., van Heijenoort, J., and Dideberg, O. 1999. Determination of the MurD mechanism through crystallographic analysis of enzyme complexes. J. Mol. Biol. 289: 579-590.
3. Bertrand, J.A., Fanchon, E., Martin, L., Chantalat, L., Auger, G., Blanot, D., van Heijenoort, J., and Dideberg, O. 2000. "Open" structures of MurD: Domain movements and structural similarities with folylpoly-glutamate synthetase. J. Mol. Biol. 301: 1257-1266.
4. Bouhss, A., Dementin, S., Parquet, C., Mengin-Lecreulx, D., Bertrand, J.A., Le Beller, D., Dideberg, O., van Heijenoort, J., and Blanot, D. 1999. Role of the ortholog and paralog amino acid invariants in the active site of the UDP-MurNAc-L-alanine:D-glutamate ligase (MurD). Biochemistry 38: 12240-12247.
5. Bugg, T.D. and Walsh, C.T. 1992. Intracellular steps of bacterial cell wall peptidoglycan biosynthesis: Enzymology, antibiotics, and antibiotic resistance. Nat. Prod. Rep. 9: 199-215.
6. Collaborative Computational Project, Number 4 (CCP4). 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.
7. El Zoeiby, A., Sanschagrin, F., and Levesque, R.C. 2003. Structure and function of the Mur enzymes: Development of novel inhibitors. Mol. Microbiol. 47: 1-12.
8. Falk, P.J., Ervin, K.M., Volk, K.S., and Ho, H.T. 1996. Biochemical evidence for the formation of a covalent acyl-phosphate linkage between UDP-N-acetylmuramate and ATP in the Escherichia coli UDP-N-acetylmuramate:L- alanine ligase-catalyzed reaction. Biochemistry 35: 1417-1422.
9. Gordon, E., Flouret, B., Chantalat, L., van Heijenoort, J., Mengin-Lecreulx, D., and Dideberg, O. 2001. Crystal structure of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: meso-diaminopimelate ligase from Escherichia coli. J. Biol. Chem. 276: 10999-11006.
10. Gu, Y.G., Florjancic, A.S., Clark, R.F., Zhang, T., Cooper, C.S., Anderson, D.D., Lerner, C.G., McCall, J.O., Cai, Y., Black-Schaefer, C.L., et al. 2004. Structure-activity relationships of novel potent MurF inhibitors. Bioorg. Med. Chem. Lett. 14: 267-270.
11. Hajduk, P.J. and Burns, D.J. 2002. Integration of NMR and high-throughput screening. Comb. Chem. High Throughput Screen 5: 613-621.
12. Hajduk, P.J., Gerfin, T., Boehlen, J.M., Haberli, M., Marek, D., and Fesik, S.W. 1999. High-throughput nuclear magnetic resonance-based screening. J. Med. Chem. 42: 2315-2317.
13. 13C-labeled methyl groups. J. Am. Chem. Soc. 122: 7898-7904.
14. Ikeda, M., Wachi, M., Jung, H., Ishino, F., and Matsuhashi, M. 1990. Homology among MurC, MurD, MurE and MurF proteins in Escherichia coli and that between E. coli MurG and a possible MurG protein in Bacillus subtilis. J. Genet. Appl. Microbiol. 36: 179-187.
15. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A Found. Crystallogr. 47: 110-119.
16. Lerner, C.G. and Beutel, B.A. 2002. Antibacterial drug discovery in the post-genomics era. Curr. Drug Targets Infect. Disord. 2: 109-119.
17. Mol, C.D., Brooun, A., Dougan, D.R., Hilgers, M.T., Tari, L.W., Wijnands, R.A., Knuth, M.W., McRee, D.E., and Swanson, R.V. 2003. Crystal structures of active fully assembled substrate- and productbound complexes of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) from Haemophilus influenzae. J. Bacteriol. 185: 4152-4162.
18. Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
19. Piotto, M., Saudek, V., and Sklenar, V. 1992. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2: 661-665.
20. Smith, C.A. and Rayment, I. 1996. Active site comparisons highlight structural similarities between myosin and other P-loop proteins. Biophys. J. 70: 1590-1602.
21. Terwilliger, T.C. and Berendzen, J. 1999. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55: 849-861.
22. van Heijenoort, J. 2001. Recent advances in the formation of the bacterial peptidoglycan monomer unit. Nat. Prod. Rep. 18: 503-519.
23. Yan, Y., Munshi, S., Leiting, B., Anderson, M.S., Chrzas, J., and Chen, Z. 2000. Crystal structure of Escherichia coli UDPMurNAc-tripeptide d-alanyl-d-alanine-adding enzyme (MurF) at 2.3 Å resolution. J. Mol. Biol. 304: 435-445.