Structure-based Mechanism of Ligand Binding for Periplasmic Solute-binding Protein of the Bug Family

Journal of Molecular Biology

Volumn 373, Issue 4, 2007, Pages 954-964

  Herrou, J ^a,b,c   Bompard, C ^b,c,d   Antoine, R ^a,b,c   Leroy, A ^e,f   Rucktooa, P ^b,c,d   Hot, D ^b,c   Huvent, I ^b,c,d   Locht, C ^a,b,c   Villeret, V ^b,c,d   Jacob Dubuisson, F ^a,b,c  

^a INSERM   (France)

^b INSTITUT PASTEUR DE LILLE   (France)

^c Molecular and Cellular Medicine   (France)

^d INSTITUT DE BIOLOGIE DE LILLE   (France)

^e UNIVERSITÉ PARIS SACLAY   (France)

^f UNIVERSITÉ DES SCIENCES ET TECHNOLOGIES DE LILLE   (France)

Author keywords

Bordetella uptake gene; crystal structure; extracytoplasmic solute receptor; mechanism of ligand binding; periplasmic transport

Indexed keywords

BENZOIC ACID; BINDING PROTEIN; CITRIC ACID; LIGAND; NICOTINAMIDE; NICOTINIC ACID; PROTEIN BUG27; QUINALDIC ACID; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BETA SHEET; CYTOPLASM; HYDROGEN BOND; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SOLUTE; STRUCTURAL PROTEOMICS;

BETAPROTEOBACTERIA; BORDETELLA; DIONAEA;

EID: 34848839194     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.08.006     Document Type: Article

References (35)

1. Lolkema J.S., Poolman B., and Konings W.N. Bacterial solute uptake and efflux systems. Curr. Opin. Microbiol. 1 (1998) 248-253
2. Saier Jr. M.H. Functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. 64 (2000) 354-411
3. Nikaido H., and Hall J.A. Overview of bacterial ABC transporters. Methods Enzymol. 292 (1998) 3-20
4. Rabus R., Jack D.L., Kelly D.J., and Saier Jr. M.H. TRAP transporters: an ancient family of extracytoplasmic solute- receptor-dependent secondary active transporters. Microbiology 145 (1999) 3145-3431
5. Winnen B., Hvorup R.N., and Saier Jr. M.H. The tripartite tricarboxylate transporter (TTT) family. Res. Microbiol. 154 (2003) 457-465
6. Dwyer M.A., and Hellinga H.W. Periplasmic binding proteins: a versatile superfamily for protein engineering. Curr. Opin. Struct. Biol. 14 (2004) 495-504
7. Felder C.B., Graul R.C., Lee A.Y., Merkle H.P., and Sadee W. The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors. AAPS PharmSci. 1 (1999) E2
8. Quiocho F.A., and Ledvina P.S. Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes. Mol. Microbiol. 20 (1996) 17-25
9. Bjorkman A.J., and Mowbray S.L. Multiple open forms of ribose-binding protein trace the path of its conformational change. J. Mol. Biol. 279 (1998) 651-664
10. Widenhorn K.A., Boos W., Somers J.M., and Kay W.W. Cloning and properties of the Salmonella typhimurium tricarboxylate transport operon in Escherichia coli. J. Bacteriol. 170 (1988) 883-888
11. Antoine R., Jacob-Dubuisson F., Drobecq H., Willery E., Lesjean S., and Locht C. Overrepresentation of a gene family encoding extracytoplasmic solute receptors in Bordetella. J. Bacteriol. 185 (2003) 1470-1474
12. Huvent I., Belrhali H., Antoine R., Bompard C., Locht C., Jacob-Dubuisson F., and Villeret V. Crystal structure of Bordetella pertussis BugD solute receptor unveils the bases of ligand binding in a new family of periplasmic binding proteins. J. Mol. Biol. 356 (2006) 1014-1026
13. Huvent I., Berhali H., Antoine R., Bompard C., Locht C., Jacob-Dubuisson F., and Villeret V. Structural analysis of the glutamate receptor BugE of Bordetella pertussis in a bound conformation. Acta Crystallog. sect. D 62 (2006) 1375-1381
14. Schneider D.R., and Parker C.D. Effect of pyridines on phenotypic properties of Bordetella pertussis. Infect. Immun. 38 (1982) 548-553
15. Melton A.R., and Weiss A.A. Characterization of environmental regulators of Bordetella pertussis. Infect. Immun. 61 (1993) 807-815
16. Melton A.R., and Weiss A.A. Environmental regulation of expression of virulence determinants in Bordetella pertussis. J. Bacteriol. 171 (1989) 6206-6212
17. Yao N., Trakhanov S., and Quiocho F.A. Refined 1.89-Å structure of the histidine-binding protein complexed with histidine and its relationship with many other active transport/chemosensory proteins. Biochemistry 33 (1994) 4769-4779
18. Trakhanov S., Vyas N.K., Luecke H., Kristensen D.M., Ma J., and Quiocho F.A. Ligand-free and -bound structures of the binding protein (LivJ) of the Escherichia coli ABC leucine/isoleucine/valine transport system: trajectory and dynamics of the interdomain rotation and ligand specificity. Biochemistry 44 (2005) 6597-6608
19. Telmer P.G., and Shilton B.H. Insights into the conformational equilibria of maltose-binding protein by analysis of high affinity mutants. J. Biol. Chem. 278 (2003) 34555-34567
20. Menozzi F.D., Mutombo R., Renauld G., Gantiez C., Hannah J.H., Leininger E., et al. Heparin-inhibitable lectin activity of the filamentous hemagglutinin adhesin of Bordetella pertussis. Infect. Immun. 62 (1994) 769-778
21. Antoine R., Alonso S., Raze D., Coutte L., Lesjean S., Willery E., et al. New virulence-activated and virulence-repressed genes identified by systematic gene inactivation and generation of transcriptional fusions in Bordetella pertussis. J. Bacteriol. 182 (2000) 5902-5905
22. Stibitz S. Use of conditionally counterselectable suicide vectors for allelic exchange. Methods Enzymol. 235 (1994) 458-465
23. Imaizumi A., Suzuki Y., Ono S., Sato Y., and Sato H. Heptakis (2,6-O-dimethyl)beta-cyclodextrin: a novel growth stimulant for Bordetella pertussis phase I. J. Clin. Microbiol. 17 (1983) 781-786
24. Doublie S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276 (1997) 523-530
25. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallog. 26 (1993) 795-800
26. Schneider T., and Sheldrick G. Substructure solution with SHELXD. Acta Crystallog. sect. D 58 (2002) 1772-1779
27. Bricogne G., Vonrhein C., Flensburg C., Schiltz M., and Paciorek W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallog. sect. D 59 (2003) 2023-2030
28. Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6 (1999) 458-463
29. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
30. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog. sect. D 60 (2004) 2126-2132
31. Brunger A.T. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallog. sect. D 49 (1993) 24-36
32. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
33. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
34. Hutchinson E.G., and Thornton J.M. PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci. 5 (1996) 212-220
35. Walmsley A.R., Shaw J.G., and Kelly D.J. The mechanism of ligand binding to the periplasmic C4-dicarboxylate binding protein (DctP) from Rhodobacter capsulatus. J. Biol. Chem. 267 (1992) 8064-8072