Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 Å resolution reveals a new fold

Proteins: Structure, Function and Genetics

Volumn 61, Issue 2, 2005, Pages 444-448

  Rife, Chris ^a,b   Schwarzenbacher, Robert ^a,c   McMullan, Daniel ^a,d   Abdubek, Polat ^a,d   Ambing, Eileen ^a,d   Axelrod, Herbert ^a,b   Biorac, Tanya ^a,d   Canaves, Jaume M ^a,c   Chiu, Hsiu Ju ^a,b   Deacon, Ashley M ^a,b   DiDonato, Michael ^a,d   Elsliger, Marc André ^a,e   Godzik, Adam ^a,c   Grittini, Carina ^a,e   Grzechnik, Slawomir K ^a,c   Hale, Joanna ^a,d   Hampton, Eric ^a,d   Han, Gye Won ^a,e   Haugen, Justin ^a,d   Hornsby, Michael ^a,d   Jaroszewski, Lukasz ^a,c   Klock, Heath E ^a,d   Koesema, Eric ^a,d   Kreusch, Andreas ^a,d   Kuhn, Peter ^a,e   Lesley, Scott A ^a,d   Miller, Mitchell D ^a,b   Moy, Kin ^a,e   Nigoghossian, Edward ^a,d   Paulsen, Jessica ^a,d   Quijano, Kevin ^a,d   Reyes, Ron ^a,b   Sims, Eric ^a,e   Spraggon, Glen ^a,d   Stevens, Raymond C ^a,e   Van Den Bedem, Henry ^a,b   Velasquez, Jeff ^a,e   Vincent, Juli ^a,d   White, Aprilfawn ^a,d   Wolf, Guenter ^a,b   Xu, Qingping ^a,b   Hodgson, Keith O ^a,b   Wooley, John ^a,c   Wilson, Ian A ^a,e   more..

^a STANFORD UNIVERSITY   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

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

^e SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; DNA TOPOISOMERASE (ATP HYDROLYSING);

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; STRUCTURE ANALYSIS; THERMOTOGA MARITIMA;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA GYRASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; THERMOTOGA MARITIMA;

BACTERIA (MICROORGANISMS); THERMOTOGA MARITIMA;

EID: 26444531033     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20468     Document Type: Article

References (18)

1. Murayama N, Shimizu H, Takiguchi S, Baba Y, Amino H, Horiuchi T, Sekimizu K, Miki T. Evidence for involvement of Escherichia coli genes pmbA, csrA and a previously unrecognized gene tldD, in the control of DNA gyrase by letD (ccdB) of sex factor F. J Mol Biol 1996;256:483-502.
2. Rodriguez-Sainz MC, Hernandez-Chico C, Moreno F. Molecular characterization of pmbA, an Escherichia coli chromosomal gene required for the production of the antibiotic peptide MccB17. Mol Microbiol 1990;4:1921-1932.
3. Yorgey P, Davagnino J, Kolter R. The maturation pathway of microcin B17, a peptide inhibitor of DNA gyrase. Mol Microbiol 1993;9:897-905.
4. 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, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Wooley J, Taylor SS, 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.
5. Matthews BW. Solvent content of protein crystals. J Mol Biol 1968;33:491-497.
6. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 2003;50: 437-450.
7. Holm L, Sander C. Dali: A network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
8. Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003;19:II246-II255.
9. 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.
10. Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants J Appl Crystallogr 1993;26:795-800.
11. Collaborative Computational Project Number 4. The CCP4 Suite: Programs for Protein Crystallography. Acta Crystallogr 1994;D50: 760-763.
12. Leslie AGW. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newslett Protein Crystallogr 1992;26.
13. Schneider TR, Sheldrick GM. Substructure solution with SHELXD. Acta Crystallogr 2002;D58:1772-1779.
14. de La Fortelle E, Bricogne G. Maximum-likelihood heavy-atom parameter refinement for the multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol 1997;276:472-494.
15. Terwilliger TC, Berendzen J. Automated structure solution for MIR and MAD. Acta Crystallogr 1999;D55:849-861.
16. Jones TA, Zou J-Y, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr 1991;D47:110-119.
17. Vriend GJ. WHAT IF: A molecular modeling and drug design program. Mol Graph 1990;8:52-56.
18. 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 1998;D54:243-252.