Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species

Protein Science

Volumn 12, Issue 2, 2003, Pages 349-360

  Smith, Kathrine J ^a   Petit, Chantal M ^b   Aubart, Kelly ^b   Smyth, Martin ^a   McManus, Edward ^c   Jones, Jo ^a   Fosberry, Andrew ^a   Lewis, Ceri ^a   Lonetto, Michael ^b   Christensen, Siegfried B ^b  

^a GLAXOSMITHKLINE   (United Kingdom)

^b GLAXOSMITHKLINE   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Crystal structure; Deformylase; Escherichia coli; Haemophilus influenzae; PDF; Staphylococcus aureus; Streptococcus pneumoniae

Indexed keywords

POLYPEPTIDE DEFORMYLASE; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CELL VIABILITY; COMPARATIVE STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG TARGETING; ENZYME ACTIVE SITE; ESCHERICHIA COLI; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HAEMOPHILUS INFLUENZAE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE;

AMIDOHYDROLASES; AMINO ACID SEQUENCE; AMINOPEPTIDASES; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; KINETICS; MICROBIAL SENSITIVITY TESTS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; NEGIBACTERIA; POSIBACTERIA; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE;

EID: 0037307109     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0229303     Document Type: Article

References (36)

1. Adams, J. 1968. On the release of the formyl group from nascent protein. J. Mol. Biol. 33: 571-589.
2. Adams, J. and Capecchi, M. 1996. The role of N-formylmethionine-s RNA as the initiator of protein synthesis. Proc. Natl. Acad. Sci. 55: 147-155.
3. Baldwin, E., Harris, M., Yem, A., Wolfe, C., Vosters, A., Curry, K., Murray, R., Bock, J., Marshall, V., Cialdella, J., et al. 2002. Crystal structure of type II peptide deformylase from Staphylococcous aureus. J. Biol. Chem. 277: 31163-31171.
4. Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., and Wagner, A. 1998a. Iron centre, substrate recognition and mechanism of peptide deformylase. Nat. Struc. Biol. 5: 1053-1058.
5. Becker, A., Schlichting, I., Kabsch, W., Schultz, S., and Wagner, A. 1998b. Structure of peptide deformylase and identification of the substrate binding site. J. Biol. Chem. 273: 11413-11416.
6. Brunger, A., Adams, P., Clore, G., DeLano, W., Gross, P., Grosse-Kunstleve, R., Jiang, J., Kuszewiski, J., Nilges, M., and Pannu, N. 1998. Crystallography and NMR system; a new software suite for macromolecular structure determination. Acta Crystallogr. D 54: 905-921.
7. Carson, M. 1991. Ribbons 2.0. Appl. Crystallography 24: 958-961.
8. CCP4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50: 760-763.
9. Chan, M., Gong, W., Ravi Rajagopalan, P., Hao, B., Tsai, C., and Pei, D. 1997. Crystal structure of the Escherichia coli peptide deformylase. Biochemistry 36: 13904-13909.
10. Clements, J., Beckett, R., Brown, A., Catlin, G., Lobell, M., Palan, S., Thomas, W., Whittaker, M., Wood, S., Salama, S., et al. 2001. Antibiotic activity and characterisation of BB-3497, a novel peptide deformylase inhibitor. Antimicrob. Agents Chemother. 2: 563-570.
11. Dardel, F., Ragusa, S., Lazennec, C., Blanquet, S., and Meinnel, T. 1998. Solution structure of nickel-peptide deformylase. J. Mol. Biol. 280: 501-513.
12. Giglione, C., Serero, A., Pierre, M., Boisson, B., and Meinnel, T. 2000. Identification of eukaryotic peptide deformylases reveals universality of N-terminal processing mechanisms. EMBO J. 19: 5916-5929.
13. Groche, D., Becker, A., Schlichting, I., Kabsch, W., Schultz, S., and Wagner, A. 1998. Isolation and crystallisation of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site. Biochem. Biophys. Res. Com. 246: 342-346.
14. Guilloteau, J.-P., Mathieu, M., Giglione, C., Blanc, V., Dupuy, A., Chevrier, M., Gil, P., Famechon, A., Meinnel, T., and Mikol, V. 2002. The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: A platform for the structure-based design of antibacterial agents. J. Mol. Biol. 320: 951-962.
15. Hao, B., Gong, W., Ravi Rajagopalan, P., Zhou, Y., Pei, D., and Chan, M. 1999. Structural basis for the design of antibiotics targeting peptide deformylase. Biochemistry 38: 4712-4719.
16. Jones, T., Zou, J.-Y., and Cowan, S. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110-119.
17. Kabsch, W., and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
18. Kumar, A., Nguyen, K., Srivathsan, S., Ornstein, B., Turley, S., Hirsh, I., Pei, D., and Hol, W. 2002. Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design. Structure 10: 357-367.
19. Lazennec, C. and Meinnel, T. 1997. Formate dehydrogenase-coupled spectrophotometric assay of peptide deformylase. Anal. Biochem. 244: 180-182.
20. Livingston, D. and Leder, P. 1969. Deformylation and protein synthesis. Biochemistry 8: 435-443.
21. Marcker, K. and Sanger, F. 1964. N-Formyl-methionyl-sRNA. J. Mol. Biol. 8: 835-840.
22. Margolis, P., Hackbarth, C., Young, D., Wang, W., Chen, D., Yuan, D., White, R., and Trias, J. 2000. Peptide deformylase in Staphylococcus aureus: Resistance to inhibition is mediated by mutations in the formyltransferase gene. Antimicrob. Agents Chemother. 44: 1825-1831.
23. Mazel, D., Pochet, S., and Marliere, P. 1994. Genetic characterisation of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J. 13: 914-923.
24. McRee, D.E. 1993. Practical protein crystallography. Academic Press, New York.
25. Meinnel, T. and Blanquet, S. 1995. Enzymatic properties of Escherichia coli peptide deformylase. J. Bacteriol. 177: 1883-1887.
26. Meinnel, T., Lazennec, C., and Blanquet, S. 1995. Mapping of the active site zinc ligands of peptide deformylase. J. Mol. Biol. 254: 175-183.
27. Meinnel, T., Lazennec, C., Villoing, S., and Blanquet, S. 1997. Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion. J. Mol. Biol. 267: 749-761.
28. O'Connell, J., Pryor, K., Grant, S., and Leiting, B. 1999. A high quality nuclear magnetic resonance solution structure of peptide deformylase from Escherichia coli: Application of an automated assignment strategy using GARANT. J. Biomol. NMR 13: 311-324.
29. Otwinowski, Z. 1993. Data collection and processing. In Proceedings of CCP4 Study Weekend. (eds. L. Sawyer et al.), pp. 56-62. SERC Daresbury Laboratory, Warrington, UK.
30. Pei, D. 2001. Peptide deformylase: A target for novel antibiotics? Emerg. Therapeut. Targets 5: 23-40.
31. Ragusa, S., Blanquet, S., and Meinnel, T. 1998. Control of peptide deformylase activity by metal cations. J. Mol. Biol. 280: 515-523.
32. Rajagopalan, P.T.R., Yu, X.C., and Pei, D. 1997. Peptide deformylase: A new type of mononuclear iron protein. J. Am. Chem. Soc. 119: 12418-12419.
33. Rajagopalan, P.T.R., Grimme, S., and Pei, D. 2000. Characterisation of cobalt (II)-substituted peptide deformylase: Function of the metal ion and the catalytic residue Glu-33. Biochemistry 39: 779-790.
34. Takeda, M. and Webster, R. 1968. Protein chain initiation and deformylation in B. subtilis homogenates. Proc. Natl. Acad. Sci. 60: 1487-1494.
35. Terwilliger, T. and Berendzen, J. 1999. Automated MAD and MIR structure solution. Acta Crystallogr. D 55: 849-861.
36. Webster, R., Engelhardt, D., and Zinder, N. 1996. In vitro protein synthesis: Chain initiation. Proc. Natl. Acad. Sci. 55: 155-161.