Compensating stereochemical changes allow murein tripeptide to be accommodated in a conventional peptide-binding protein

Journal of Biological Chemistry

Volumn 286, Issue 36, 2011, Pages 31512-31521

  Maqbool, Abbas ^a   Levdikov, Vladimir M ^a   Blagova, Elena V ^a   Hervé, Mireille ^b,c   Horler, Richard S P ^a,d   Wilkinson, Anthony J ^a   Thomas, Gavin H ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

^b UNIVERSITÉ PARIS SACLAY   (France)

^c CNRS   (France)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO GROUP; ATP-BINDING CASSETTE TRANSPORTERS; CELL-WALL COMPONENTS; D-AMINO ACID; DIAMINOPIMELIC ACIDS; FUNCTIONAL TRANSPORTERS; HIGH AFFINITY; MAIN CHAINS; MEMBRANE COMPONENTS; OLIGOPEPTIDES; PEPTIDE BONDS; PEPTIDE LIGAND; PEPTIDE LINKAGES; PEPTIDE-BINDING; POLAR RESIDUES; SIDE-CHAINS; STEREOCHEMICAL CHANGES; SUBSTRATE-BINDING; TRI-PEPTIDES; TRIPEPTIDE;

AMINO ACIDS; CARBOXYLATION; CRYSTAL STRUCTURE; ESCHERICHIA COLI; STEREOCHEMISTRY;

PEPTIDES;

ALANINE GAMMA DEXTRO GLUTAMIC ACID MESO DIAMINOPIMELATE; BINDING PROTEIN; DIAMINOPIMELIC ACID; GLUTAMIC ACID; OLIGOPEPTIDE PERMEASE; PERMEASE; PROTEIN MPPA; TRIPEPTIDE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIPOLE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; STEREOCHEMISTRY; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; CARRIER PROTEINS; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; LIPOPROTEINS; MEMBRANE TRANSPORT PROTEINS; OLIGOPEPTIDES; PEPTIDOGLYCAN; PROTEIN CONFORMATION; STEREOISOMERISM;

ESCHERICHIA COLI;

EID: 80052398962     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.267179     Document Type: Article

References (39)

1. Detmers, F. J., Lanfermeijer, F. C., and Poolman, B. (2001) Res. Microbiol. 152, 245-258
2. Doeven, M. K., Kok, J., and Poolman, B. (2005) Mol. Microbiol. 57, 640-649
3. Berntsson, R. P., Smits, S. H., Schmitt, L., Slotboom, D. J., and Poolman, B. (2010) FEBS Lett. 584, 2606-2617
4. Guyer, C. A., Morgan, D. G., and Staros, J. V. (1986) J. Bacteriol. 168, 775-779
5. Smith, M. W., Tyreman, D. R., Payne, G. M., Marshall, N. J., and Payne, J. W. (1999) Microbiology 145, 2891-2901
6. Tame, J. R., Murshudov, G. N., Dodson, E. J., Neil, T. K., Dodson, G. G., Higgins, C. F., and Wilkinson, A. J. (1994) Science 264, 1578-1581
7. Sleigh, S. H., Tame, J. R., Dodson, E. J., and Wilkinson, A. J. (1997) Biochemistry 36, 9747-9758
8. Dunten, P., and Mowbray, S. L. (1995) Protein Sci. 4, 2327-2334
9. Nickitenko, A. V., Trakhanov, S., and Quiocho, F. A. (1995) Biochemistry 34, 16585-16595
10. Sleigh, S. H., Seavers, P. R., Wilkinson, A. J., Ladbury, J. E., and Tame, J. R. (1999) J. Mol. Biol. 291, 393-415
11. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., and Shao, Y. (1997) Science 277, 1453-1462
12. Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K., Blattner, F. R., Chaudhuri, R. R., Glasner, J. D., Horiuchi, T., Keseler, I. M., Kosuge, T., Mori, H., Perna, N. T., Plunkett, G., 3rd, Rudd, K. E., Serres, M. H., Thomas, G. H., Thomson, N. R., Wishart, D., and Wanner, B. L. (2006) Nucleic Acids Res. 34, 1-9
13. Park, J. T., Raychaudhuri, D., Li, H., Normark, S., and Mengin-Lecreulx, D. (1998) J. Bacteriol. 180, 1215-1223
14. Park, J. T., and Uehara, T. (2008) Microbiol. Mol. Biol. Rev. 72, 211-227
15. Lessard, I. A., Pratt, S. D., McCafferty, D. G., Bussiere, D. E., Hutchins, C., Wanner, B. L., Katz, L., and Walsh, C. T. (1998) Chem. Biol. 5, 489-504
16. Suzuki, H., Koyanagi, T., Izuka, S., Onishi, A., and Kumagai, H. (2005) J. Bacteriol. 187, 5861-5867
17. Leonard, B. A., Podbielski, A., Hedberg, P. J., and Dunny, G. M. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 260-264
18. Fogg, M. J., and Wilkinson, A. J. (2008) Biochem. Soc. Trans. 36, 771-775
19. Zheng, L., Baumann, U., and Reymond, J. L. (2004) Nucleic Acids Res. 32, e115
20. Tame, J. R., Dodson, E. J., Murshudov, G., Higgins, C. F., and Wilkinson, A. J. (1995) Structure 3, 1395-1406
21. Lanfermeijer, F. C., Picon, A., Konings, W. N., and Poolman, B. (1999) Biochemistry 38, 14440-14450
22. Brzozowski, A. M., and Walton, J. (2001) J. Appl. Crystallogr. 34, 97-101
23. Vagin, A., and Teplyakov, A. (2000) Acta Crystallogr. D Biol. Crystallogr. 56, 1622-1624
24. Emsley, P., and Cowtan, K. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
25. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
26. Hervé, M., Boniface, A., Gobec, S., Blanot, D., and Mengin-Lecreulx, D. (2007) J. Bacteriol. 189, 3987-3995
27. Pennartz, A., Généreux, C., Parquet, C., Mengin-Lecreulx, D., and Joris, B. (2009) Antimicrob. Agents Chemother. 53, 2991-2997
28. Holm, L., Kääriäinen, S., Rosenström, P., and Schenkel, A. (2008) Bioinformatics 24, 2780-2781
29. Berntsson, R. P., Doeven, M. K., Fusetti, F., Duurkens, R. H., Sengupta, D., Marrink, S. J., Thunnissen, A. M., Poolman, B., and Slotboom, D. J. (2009) EMBO J. 28, 1332-1340
30. Levdikov, V. M., Blagova, E. V., Brannigan, J. A., Wright, L., Vagin, A. A., and Wilkinson, A. J. (2005) J. Mol. Biol. 345, 879-892
31. Severi, E., Randle, G., Kivlin, P., Whitfield, K., Young, R., Moxon, R., Kelly, D., Hood, D., and Thomas, G. H. (2005) Mol. Microbiol. 58, 1173-1185
32. Thomas, G. H., Southworth, T., León-Kempis, M. R., Leech, A., and Kelly, D. J. (2006) Microbiology 152, 187-198
33. Payne, J. W. (1971) Biochem. J. 123, 245-253
34. Létoffé, S., Delepelaire, P., and Wandersman, C. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 12891-12896
35. Williams, W. A., Zhang, R. G., Zhou, M., Joachimiak, G., Gornicki, P., Missiakas, D., and Joachimiak, A. (2004) Biochemistry 43, 16193-16202
36. Nanavati, D. M., Thirangoon, K., and Noll, K. M. (2006) Appl. Environ. Microbiol. 72, 1336-1345
37. Cuneo, M. J., Beese, L. S., and Hellinga, H. W. (2009) J. Biol. Chem. 284, 33217-33223
38. Goodell, E. W., and Schwarz, U. (1985) J. Bacteriol. 162, 391-397
39. Uehara, T., and Park, J. T. (2007) J. Bacteriol. 189, 5634-5641