Crystal structure of a bacterial signal peptidase in complex with a β- lactam inhibitor

Nature

Volumn 396, Issue 6707, 1998, Pages 186-190

  Paetzel, Mark ^a   Dalbey, Ross E ^b   Strynadka, Natalie C J ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLYL (5,6) 6 (ACETOXYETHYL)PENEM 3 CARBOXYLIC ACID; BETA LACTAM ANTIBIOTIC; PROTEINASE; SIGNAL PEPTIDASE; UNCLASSIFIED DRUG;

ARTICLE; CELL VIABILITY; CRYSTAL STRUCTURE; ENZYME STRUCTURE; ESCHERICHIA COLI; HYDROGEN BOND; MEMBRANE BINDING; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; BETA-LACTAMS; BINDING SITES; CARBOXYLIC ACIDS; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; LACTAMS; MEMBRANE PROTEINS; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; SERINE; SERINE ENDOPEPTIDASES; SERINE PROTEINASE INHIBITORS;

EID: 0032511889     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/24196     Document Type: Article

References (30)

1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 signal peptidases. Protein Sci. 6, 1129-1138 (1997).
2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274-280 (1993).
3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935-3941 (1995).
4. Allsop, A. E. et al. in Anti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationship (eds Bently, P. H. & O'Hanlon, P. J.) 61-72 (R. Soc. Chem., Cambridge, 1997).
5. Black, M. T. & Bruton, G. Inhibitors of bacterial signal peptidases. Curr. Pharm. Des. 4, 133-154 (1998).
6. Date, T. Demonstration by a novel genetic technique that leader peptidase is an essential enzyme in Escherichia coli. J. Bacteriol. 154, 76-83 (1983).
7. . Whitely, P. & von Heijne, G. The DsbA-DsbB system affects the formation of disulfide bonds in periplasmic but not in intramembraneous protein domains. FEBS Lett. 332, 49-51 (1993).
8. Peat, T. S. et al. Structure of the UmuD′ protein and its regulation in response to DNA damage. Nature 380, 727-730 (1996).
9. Paetzel, M. et al. Crystallization of a soluble, catalytically active form of Escherichia coli leader peptidase. Proteins Struct. Funct. Genet. 23, 122-125 (1995).
10. van Klompenburg, W. et al. Phosphatidylethanolamine mediated insertion of the catalytic domain of leader peptidase in membranes. FEBS Lett. 431, 75-79 (1998).
11. Kim, Y. T., Muramatsu, T. & Takahashi, K. Identification of Trp 300 as an important residue for Escherichia coli leader peptidase activity. Eur. J. Biochem. 234, 358-362 (1995).
12. Landolt-Marticorena, C., Williams, K. A., Deber, C. M. & Reithmeirer, R. A. Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. J. Mol. Biol. 229, 602-608 (1993).
13. James, M. N. G. in Proteolysis and Protein Turnover (eds Bond, J. S. & Barrett, A. J.) 1-8 (Portland, Brookfield, VT, 1994).
14. Strynadka, N. C. J. et al. Molecular structure of the acyl-enzyme intermediate in β-lactamase at 1.7 Å resolution. Nature 359, 393-400 (1992).
15. Manard, R. & Storer, A. C. Oxyanion hole interactions in serine and cysteine proteases. Biol. Chem. Hoppe-Seyler 373, 393-400 (1992).
16. Nicolas, A. et al. Contribution of cutinase Ser 42 side chain to the stabilization of the oxyamon transition state. Biochemistry 35, 398-410 (1996).
17. Paetzel, M. et al. Use of site-directed chemical modification to study an essential lysine in Escherichia coli leader peptidase. J. Biol. Chem. 272, 9994-10003 (1997).
18. Paetzel, M. & Dalbey, R. E. Catalytic hydroxyl/amine dyads with serine proteases. Trends Biochem. Sci. 22, 28-31 (1997).
19. von Heijne, G. Signal sequences. The limits of variation. J. Mol. Biol. 184, 99-105 (1985).
20. Izard, J. W. & Kendall, D. A. Signal peptides: exquisitely designed transport promoters. Mol. Microbiol. 13, 765-773 (1994).
21. Matthews, B. W. Solvent content of protein crystals. J. Mol. Biol. 33, 491-497 (1968).
22. Otwinowski, Z. in DENZO (eds Sawyer, L., Isaacs, N. & Baily, S.) 56-62 (SERC Daresbury Laboratory, Warrington, UK, 1993).
23. Collaborative Computational Project No. 4 The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
24. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kieldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
25. Brunger, A. T. X-PLOR: A System for X-ray Crystallography and NMR (Version 3.1) (Yale Univ. Press, New Haven, 1987).
26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the refinement of macromolecules. Acta Crystallogr. A 48, 912-916 (1992).
27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073-12080 (1983).
28. Kraulis, P. G. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950 (1991).
29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281-296 (1991).
30. Meritt, E. A. & Bacon, D. J. Raster3TD: photorealistic molecular graphics. Methods Enzymol. 277, 505-524 (1997).