Solution structure of nickel-peptide deformylase

Journal of Molecular Biology

Volumn 280, Issue 3, 1998, Pages 501-513

  Dardel, Frédéric ^a   Ragusa, Stéphane ^a   Lazennec, Christine ^a   Blanquet, Sylvain ^a   Meinnel, Thierry ^a  

^a LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

Formyl; Metalloprotease; NMR; Thermolysin; Zinc

Indexed keywords

ARGININE; BACTERIAL ENZYME; GLYCINE; METALLOPROTEINASE; NICKEL; PEPTIDE; THERMOLYSIN; ZINC;

ALPHA HELIX; ARTICLE; BETA CHAIN; ENZYME ACTIVITY; ENZYME STRUCTURE; GENETIC CONSERVATION; HYDROLYSIS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS;

EID: 0032540851     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1882     Document Type: Article

References (36)

1. Amann E., Ochs B., Abel K.-J. Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli. Gene. 69:1988;301-315
2. β resonances in larger proteins. J. Magn. Reson. 95:1991;636-641
3. 13C-enriched proteins. J. Magn. Reson. 88:1990;425-431
4. 3 angular information from long-range proton-carbon and carbon-carbon J correlation in a calmodulin-peptide complex. J. Biomol. NMR. 4:1994;787-797
5. Blundell T.L. Metalloproteinase super-family and drug design. Nature Struct. Biol. 1:1994;73-75
6. Browner M.F., Smith W.W., Castelhano A.L. Matrilysin inhibitor complexes common themes among metalloproteases. Biochemistry. 34:1995;6602-6610
7. Brünger A.T. X-PLOR Version 3. 1. A system for X-ray Crystallography and NMR. 1992;Yale University Press, New Haven and London
8. Chan M.K., Gong W., Rajagopalan P.T.R., Tsai C.M., Pei D. Crystal structure of Escherichia coli peptide deformylase. Biochemistry. 36:1997;13904-13909
9. Clore G.M., Gronenborn A.M., Nilges M., Ryan C.A. The three dimensional structure of potato carboxypeptidase inhibitor in solution a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics. Biochemistry. 26:1987;8012-8023
10. Fejzo J., Westler W.M., Macura S., Markley J.L. Strategies for eliminating unwanted cross-relaxation and coherence-transfer effects from two-dimensional chemical-exchange spectra. J. Magn. Reson. 92:1991;20-29
11. Gargaro A.R., Frenkiel T.A., Nieto P.M., Birdsall B., Polshakov V.I., Morgan W.D., Feeney J. NMR detection of arginine-ligand interactions in complexes of Lactobacillus casei dihydrofolate reductase. Eur. J. Biochem. 238:1996;435-439
12. Güntert P., Wüthrich K. Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J. Mol. Biol. 1:1991;447-456
13. Güntert P., Braun W., Wüthrich K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217:1991;517-530
14. Higgins D.G., Sharp P.M. Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Applic. Biosci. 5:1989;151-153
15. Holmes M.A., Matthews B.W. Structure of thermolysin refined at 1.6 Å resolution. J. Mol. Biol. 160:1982;623-629
16. Kay L.E., Ikura M., Tschudin R., Bax A. Three-dimensional triple resonance NMR spectroscopy of isotopically enriched proteins. J. Magn. Reson. 89:1990;496-514
17. Lazennec C., Meinnel T. Formate dehydrogenase-coupled spectrophotometric assay of peptide deformylase. Anal. Biochem. 244:1997;180-182
18. Met formyltransferase are encoded within the same operon in Escherichia coli. J. Bacteriol. 175:1993;7737-7740
19. Met formyltransferase. J. Bacteriol. 176:1994;7387-7390
20. Meinnel T., Mechulam Y., Blanquet S. Methionine as translation start signal a review of the enzymes of the pathway in Escherichia coli. Biochimie (Paris). 75:1993;1061-1075
21. Meinnel T., Lazennec C., Blanquet S. Mapping of the active site zinc ligands of peptide deformylase. J. Mol. Biol. 254:1995;175-183
22. Meinnel T., Blanquet S., Dardel F. A new subclass of the zinc metalloproteases family revealed by the solution structure of peptide deformylase. J. Mol. Biol. 262:1996;375-386
23. Meinnel T., Lazennec C., Dardel F., Schmitter J.-M., Blanquet S. The C-terminal domain of peptide deformylase is disordered and dispensable for activity. FEBS Letters. 385:1996;91-95
24. Meinnel T., Lazennec C., Villoing S., Blanquet S. Structure-function relationships of the peptide deformylase family. Evidence for a common tertiary fold of the active site built around three conserved motifs and a metal ion. J. Mol. Biol. 267:1997;749-761
25. Nieto P.M., Birdsall B., Morgan W.D., Frenkiel T.A., Gargaro A.R., Feeney J. Correlated rotations in interactions of arginine residues with ligands carboxylate groups in protein ligand complexes. FEBS Letters. 405:1997;16-20
26. Glc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques. Protein Sci. 2:1993;543-558
27. Ragusa S., Blanquet S., Meinnel T. Control of peptide deformylase activity by metal cations. J. Mol. Biol. 280:1998;515-523
28. Rawlings N.D., Barrett A.J. Evolutionary families of metallopeptidases. Methods Enzymol. 248:1995;183-228
29. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA. 74:1977;5463-5467
30. Sayers J.R., Schmidt W., Eckstein F. 5′→3′ exonuclease in phosphorothioate-based oligonucleotide-directed mutagenesis. Nucl. Acids Res. 16:1988;791-802
31. Seavey B.R., Farr E.A., Westler W.M., Markley J.L. A relational database for sequence-specific protein NMR data. J. Biomol. NMR. 1:1991;217-236
32. Stöcker W., Grams F., Baumann U., Reinemer P., Gomis-Ruth F.-X., McKay D.B., Bode W. The metzincins-topological and sequential relations between the astacins, adamalysins, serralysins and matrixins (collagenases) define a superfamily of zinc-peptidases. Protein Sci. 4:1995;823-840
33. 13C-enriched proteins by homonuclear broadband decoupling. J. Magn. Reson. 98:1992;428-435
34. Wagner G., Braun W., Havel T.F., Schauman T., Go N., Wuthrich K. Protein structure in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined by two different algorithms DISGEO and DISMAN. J. Mol. Biol. 196:1987;611-639
35. Weaver L.H., Kester W.R., Matthews B.W. A crystallographic study of the complex of phosphoramidon with thermolysin. A model for the presumed catalytic transition state and for the binding of extended substrates. J. Mol. Biol. 114:1977;119-132
36. Zuiderweg E.R.P., Fesik S.W. Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a. Biochemistry. 28:1989;2387-2391