Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 Å resolution

Proteins: Structure, Function and Genetics

Volumn 67, Issue 1, 2007, Pages 247-252

  Weekes, Dana ^a,b   Miller, Mitchell D ^a,e   Sri Krishna, S ^a,b,c   McMullan, Daniel ^a,d   McPhillips, Timothy M ^a,e   Acosta, Claire ^a,d   Canaves, Jaume M ^a,c   Elsliger, Marc André ^a,f   Floyd, Ross ^a,e   Grzechnik, Slawomir K ^a,c   Jaroszewski, Lukasz ^a,b,c   Klock, Heath E ^a,d   Koesema, Eric ^a,d   Kovarik, John S ^a,e   Kreusch, Andreas ^a,d   Morse, Andrew T ^a,c   Quijano, Kevin ^a,d   Spraggon, Glen ^a,d   Van Den Bedem, Henry ^a,e   Wolf, Guenter ^a,e   Hodgson, Keith O ^a,e   Wooley, John ^a,c   Deacon, Ashley M ^a,e   Godzik, Adam ^a,b,c   Lesley, Scott A ^a,d,f   Wilson, Ian A ^a,f   more..

^a Joint Center for Structural Genomics   (United States)

^b BURNHAM INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^e SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^f SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL PROTEIN; DNA BINDING PROTEIN; GENOMIC DNA; HISTIDINE; REGULATOR PROTEIN; TM1602 PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; CRYSTAL STRUCTURE; DNA BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN STRUCTURE; THERMOTOGA MARITIMA; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; THERMOTOGA MARITIMA; TRANSCRIPTION FACTORS;

THERMOTOGA MARITIMA;

EID: 33847397866     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21221     Document Type: Article

References (31)

1. Anantharaman V, Koonin EV, Aravind L. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol 2001;307:1271-1292.
2. Rossolillo P, Marinoni I, Galli E, Colosimo A, Albertini AM. YrxA is the transcriptional regulator that represses de novo NAD biosynthesis in Bacillus subtilis. J Bacteriol 2005;187:7155-7160.
3. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA 2002;99:11664-11669.
4. Santarsiero BD, Yegian DT, Lee CC, Spraggon G, Gu J, Scheibe D, Uber DC, Cornell EW, Nordmeyer RA, Kolbe WF, Jin J, Jones AL, Jaklevic JM, Schultz PG, Stevens RC. An approach to rapid protein crystallization using nanodroplets. J Appl Crystallogr 2002;35:278-281.
5. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994;50:760-763.
6. Tickle IJ, Laskowski RA, Moss DS. Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of γB- and βB2-crystallin. Acta Crystallogr D Biol Crystallogr 1998;54:243-252.
7. McPhillips TM, McPhillips SE, Chiu HJ, Cohen AE, Deacon AM, Ellis PJ, Garman E, Gonzalez A, Sauter NK, Phizackerley RP, Soltis SM, Kuhn P. Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J Synchrotron Radiat 2002;9:401-406.
8. Leslie AGW. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4+ESF-EAMCB Newsletter on Protein Crystallography, No. 26. 1992.
9. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1999;55:849-861.
10. Cohen SX, Morris RJ, Fernandez FJ, Ben Jelloul M, Kakaris M, Parthasarathy V, Lamzin VS, Kleywegt GJ, Perrakis A. Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr D Biol Crystallogr 2004;60:2222-2229.
11. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
12. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
13. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD. Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2004;60:1833-1839.
14. Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 2004;32: W615-W619.
15. Vaguine AA, Richelle J, Wodak SJ. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 1999;55:191-205.
16. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990;8:52-56, 29.
17. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
18. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
19. Castagnetto JM, Hennessy SW, Roberts VA, Getzoff ED, Tainer JA, Pique ME. MDB: the metalloprotein database and browser at the Scripps Research Institute. Nucleic Acids Res 2002;30:379-382.
20. Holm L, Sander C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
21. Waygood EB. The structure and function of HPr. Biochem Cell Biol 1998;76:359-367.
22. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
23. Kaplan DR, Stephens RM. Neurotrophin signal transduction by the Trk receptor. J Neurobiol 1994;25:1404-1417.
24. + efflux. FEMS Microbiol Lett 2001;204:61-64.
25. + in bacterial transport. Mol Microbiol 1993;9:533-543.
26. Penfound T, Foster JW. NAD-dependent DNA-binding activity of the bifunctional NadR regulator of Salmonella typhimurium. J Bacteriol 1999;181:648-655.
27. Raffaelli N, Lorenzi T, Mariani PL, Emanuelli M, Amici A, Ruggieri S, Magni G. The Escherichia coli NadR regulator is endowed with nicotinamide mononucleotide adenylyltransferase activity. J Bacteriol 1999;181:5509-5511.
28. Grose JH, Bergthorsson U, Roth JR. Regulation of NAD synthesis by the trifunctional NadR protein of Salmonella enterica. J Bacteriol 2005;187:2774-2782.
29. Gerasimova AV, Gelfand MS. Evolution of the NadR regulon in Enterobacteriaceae. J Bioinform Comput Biol 2005;3:1007-1019.
30. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R. The TetR family of transcriptional repressors. Microbiol Mol Biol Rev 2005;69:326-356.
31. Vesterstrom J, Taylor WR. Flexible secondary structure based protein structure comparison applied to the detection of circular permutation. J Comput Biol 2006;13:43-63.