A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor

Proteins: Structure, Function and Genetics

Volumn 71, Issue 4, 2008, Pages 2038-2050

  Doan, Thierry ^a   Martin, Laetitia ^b   Zorrilla, Silvia ^b   Chaix, Denis ^a,b   Aymerich, Stéphane ^a   Labesse, Gilles ^b   Declerck, Nathalie ^b,c  

^a CNRS   (France)

^b INSERM   (France)

^c CENTRE DE BIOCHIMIE STRUCTURALE   (France)

Author keywords

Bacillus subtilis; Carbon metabolism; Fluorescence anisotropy; Ligand screening; Molecular modeling; Site directed mutagenesis; Transcriptional regulation

Indexed keywords

ARGININE; BACTERIAL ENZYME; BACTERIAL ENZYME NAGB; DEAMINASE; DNA; FRUCTOSE 1,6 BISPHOSPHATE; GLUCOSAMINE 6 PHOSPHATE DEAMINASE; SUGAR PHOSPHATE; TRYPSIN;

ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; DNA BINDING; DNA BINDING MOTIF; ENZYME STRUCTURE; GENE CONTROL; GENE REPRESSION; GLYCOLYSIS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN INTERACTION; SCREENING; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

ALDOSE-KETOSE ISOMERASES; AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BINDING SITES; CIRCULAR DICHROISM; COMPUTER SIMULATION; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; ESCHERICHIA COLI; FLUORESCENCE POLARIZATION; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; OPERON; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROPHOTOMETRY, ULTRAVIOLET; STRUCTURE-ACTIVITY RELATIONSHIP;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

EID: 44349160732     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21883     Document Type: Article

References (29)

1. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Danchin A, Daniel A, Denizot F, Devine KM, Düsterhöft A, Ehrlich SD, Emmerson PT, Entian KD, Errington J, Fabret C, Ferrari E, Foulger D, Fritz C, Fujita M, Fujita Y, Fuma S, Galizzi A, Galleron N, Ghim S-Y, Glaser P, Goffeau A, Golightly EJ, Grandi G, Guiseppi G, Guy BJ, Haga K, Haiech J, Harwood CR, Hénaut A, Hubert H, Holsappel S, Hosono S, Hullo M-F, Itaya M, Jones L, Joris B, Karamata D, Kasahara Y, Klaerr-Blanchard M, Klein C, Kobayashi Y, Koetter P, Koningstein G, Krogh S, Kumano M, Kurita K, Lapidus A, Lardinois S, Lauber J, Lazarevic V, Lee S-M, Levine A, Liu H, Masuda S, Mauël C, Médigue C, Medina N, Mellado RP, Mizuno M, Moestl D, Nakai S, Noback M, Noone D, O'Reilly M, Ogawa K, Ogiwara A, Oudega B, Park S-H, Parro V, Pohl TM, Portetelle D, Porwollik S, Prescott AM, Presecan E, Pujic P, Purnelle B, Rapoport G, Rey M, Reynolds S, Rieger M, Rivolta C, Rocha E, Roche B, Rose M, Sadaie Y, Sato T, Scanlan E, Schleich S, Schroeter R, Scoffone F, Sekiguchi J, Sekowska A, Seror SJ, Serror P, Shin B-S, Soldo B, Sorokin A, Tacconi E, Takagi T, Takahashi H, Takemaru K, Takeuchi M, Tamakoshi A, Tanaka T, Terpstra P, Tognoni A, Tosato V, Uchiyama S, Vandenbol M, Vannier F, Vassarotti A, Viari A, Wambutt R, Wedler E, Wedler H, Weitzenegger T, Winters P, Wipat A, Yamamoto H, Yamane K, Yasumoto K, Yata K, Yoshida K, Yoshikawa H-F, Zumstein E, Yoshikawa H. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 1997;390:249-256.
2. Fillinger S, Boschi-Muller S, Azza S, Dervyn E, Branlant G, Aymerich S. Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem 2000;275:14031-14037.
3. Ludwig H, Homuth G, Schmalisch M, Dyka FM, Hecker M, Stulke J. Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon. Mol Microbiol 2001;41:409-422.
4. Tobisch S, Zuhlke D, Bernhardt J, Stulke J, Hecker M. Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis. J Bacteriol 1999;181:6996-7004.
5. Doan T, Aymerich S. Regulation of the central glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate. Mol Microbiol 2003;47:1709-1721.
6. Zorrilla S, Doan T, Alfonso C, Margeat E, Ortega A, Rivas G, Aymerich S, Royer CA, Declerck N. Inducer-modulated cooperative binding of the tetrameric CggR repressor to operator DNA. Biophys J 2007;92:3215-3227.
7. Wohrl BM, Wehmeier UF, Lengeler JW. Positive and negative regulation of expression of the L-sorbose (sor) operon by SorC in Klebsiella pneumoniae. Mol Gen Genet 1990;224:193-200.
8. Heuel H, Shakeri-Garakani A, Turgut S, Lengeler JW. Genes for D-arabinitol and ribitol catabolism from Klebsiella pneumoniae. Microbiology 1998;144 (Part 6):1631-1639.
9. Sangari FJ, Aguero J, Garcia-Lobo JM. The genes for erythritol catabolism are organized as an inducible operon in Brucella abortus. Microbiology 2000;146 (Part 2):487-495.
10. Yebra MJ, Veyrat A, Santos MA, Perez-Martinez G. Genetics of L-sorbose transport and metabolism in Lactobacillus casei. J Bacteriol 2000;182:155-163.
11. Zeng X, Saxild HH, Switzer RL. Purification and characterization of the DeoR repressor of Bacillus subtilis. J Bacteriol 2000;182:1916-1922.
12. Anagnostopoulos C, Spizizen J. Requirements for transformation in Bacillus subtilis. J Bacteriol 1961;81:741-746.
13. Aymerich S, Gonzy-Treboul G, Steinmetz M. 5′-noncoding region sacR is the target of all identified regulation affecting the levansucrase gene in Bacillus subtilis. J Bacteriol 1986;166:993-998.
14. Guerout-Fleury AM, Frandsen N, Stragier P. Plasmids for ectopic integration in Bacillus subtilis. Gene 1996;180:57-61.
15. Royer CA, Smith WR, Beechem JM. Analysis of binding in macromolecular complexes: a generalized numerical approach. Anal Biochem 1990;191:287-294.
16. Labesse G, Mornon J. Incremental threading optimization (TITO) to help alignment and modeling of remote homologues. Bioinformatics 1998;14:206-211.
17. Canutescu AA, Shelenkov AA, Dunbrack RL, Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
18. Rarey M, Wefing S, Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des 1996;10:41-54.
19. Jain AN. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 2003;46:499-511.
20. Wang R, Lai L, Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 2002;16:11-26.
21. van Aalten DM, Bywater R, Findlay JB, Hendlich M, Hooft RW, Vriend G. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J Comput Aided Mol Des 1996;10:255-262.
22. Gouet P, Courcelle E, Stuart DI, Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 1999;15:305-308.
23. Rudino-Pinera E, Morales-Arrieta S, Rojas-Trejo SP, Horjales E. Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminase. Acta Crystallogr D Biol Crystallogr 2002;58 (Part 1):10-20.
24. Vincent F, Davies GJ, Brannigan JA. Structure and kinetics of a monomeric glucosamine 6-phosphate deaminase: missing link of the NagB superfamily? J Biol Chem 2005;280:19649-19655.
25. Horjales E, Altamirano MM, Calcagno ML, Garratt RC, Oliva G. The allosteric transition of glucosamine-6-phosphate deaminase: the structure of the T state at 2.3-Å resolution. Structure 1999;7:527-537.
26. Bustos-Jaimes I, Sosa-Peinado A, Rudino-Pinera E, Horjales E, Calcagno ML. On the role of the conformational flexibility of the active-site lid on the allosteric kinetics of glucosamine-6-phosphate deaminase. J Mol Biol 2002;319:183-189.
27. Oliva G, Fontes MR, Garratt RC, Altamirano MM, Calcagno ML, Horjales E. Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 A resolution. Structure 1995;3:1323-1332.
28. Hamada K, Ago H, Sugahara M, Nodake Y, Kuramitsu S, Miyano M. Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi). J Biol Chem 2003;278:49183-49190.
29. Titgemeyer F, Reizer J, Reizer A, Saier MH, Jr. Evolutionary relationships between sugar kinases and transcriptional repressors in bacteria. Microbiology 1994;140 (Part 9):2349-2354.