High resolution crystal structure of Sco5413, a widespread actinomycete MarR family transcriptional regulator of unknown function

Proteins: Structure, Function and Bioinformatics

Volumn 81, Issue 1, 2013, Pages 176-182

  Holley, Tracey A ^a   Stevenson, Clare E M ^a   Bibb, Mervyn J ^a   Lawson, David M ^a  

^a JOHN INNES CENTRE   (United Kingdom)

Author keywords

Antibiotic biosynthesis; Protein DNA interactions; Protein ligand interactions; Streptomyces coelicolor; Winged helix fold

Indexed keywords

ANTIBIOTIC AGENT; BACTERIAL PROTEIN; DIMER; HOMODIMER; LIGAND;

ACTINOBACTERIA; ARTICLE; BACTERIAL GROWTH; BINDING SITE; CRYSTAL STRUCTURE; DNA BINDING; GENE SEQUENCE; GENOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN STRUCTURE; STREPTOMYCES COELICOLOR; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA-BINDING PROTEINS; GENOME, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; STREPTOMYCES COELICOLOR; STRUCTURAL HOMOLOGY, PROTEIN; TRANSCRIPTION FACTORS;

STREPTOMYCES COELICOLOR;

EID: 84871091704     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24197     Document Type: Article

References (22)

1. Perera IC, Grove A. Molecular mechanisms of ligand-mediated attenuation of DNA binding by MarR family transcriptional regulators. J Mol Cell Biol 2010; 2: 243-254.
2. Alekshun MN, Levy SB, Mealy TR, Seaton BA, Head JF. The crystal structure of MarR, a regulator of multiple antibiotic resistance, at 2.3 Å resolution. Nat Struct Biol 2001; 8: 710-714.
3. Hong M, Fuangthong M, Helmann JD, Brennan RG. Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Mol Cell 2005; 20: 131-141.
4. Newberry KJ, Fuangthong M, Panmanee W, Mongkolsuk S, Brennan RG. Structural mechanism of organic hydroperoxide induction of the transcription regulator OhrR. Mol Cell 2007; 28: 652-664.
5. Palm GJ, Khanh Chi B, Waack P, Gronau K, Becher D, Albrecht D, Hinrichs W, Read RJ, Antelmann H. Structural insights into the redox-switch mechanism of the MarR/DUF24-type regulator HypR. Nucleic Acids Res 2012; 40: 4178-4192.
6. Dolan KT, Duguid EM, He C. Crystal structures of SlyA protein, a master virulence regulator of Salmonella, in free and DNA-bound states. J Biol Chem 2011; 286: 22178-22185.
7. Winter G. Xia2: an expert system for macromolecular crystallography data reduction. J Appl Crystallogr 2010; 43: 186-190.
8. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr Sect D 2010; 66: 213-221.
9. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr Sect D 2008; 64: 61-69.
10. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr Sect D 1997; 53: 240-255.
11. Cowtan K. Recent developments in classical density modification. Acta Crystallogr Sect D 2010; 66: 470-478.
12. Cowtan K. The Buccaneer software for automated model building. I. Tracing protein chains. Acta Crystallogr Sect D 2006; 62: 1002-1011.
13. Perrakis A, Morris R, Lamzin VS. Automated protein model building combined with iterative structure refinement. Nat Struct Biol 1999; 6: 458-463.
14. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D 2004; 60: 2126-2132.
15. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, 3rd, Snoeyink J, Richardson JS, Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 2007; 35: W375-W383.
16. DeLano WL. The PyMOL user's manual. San Carlos, CA, USA: DeLano Scientific; 2002.
17. Gajiwala KS, Burley SK. Winged helix proteins. Curr Opin Struct Biol 2000; 10: 110-116.
18. Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr Sect D 2004; 60: 2256-2268.
19. Di Fiore A, Fiorentino G, Vitale RM, Ronca R, Amodeo P, Pedone C, Bartolucci S, De Simone G. Structural analysis of BldR from Sulfolobus solfataricus provides insights into the molecular basis of transcriptional activation in Archaea by MarR family proteins. J Mol Biol 2009; 388: 559-569.
20. Bordelon T, Wilkinson SP, Grove A, Newcomer ME. The crystal structure of the transcriptional regulator HucR from Deinococcus radiodurans reveals a repressor preconfigured for DNA binding. J Mol Biol 2006; 360: 168-177.
21. Saridakis V, Shahinas D, Xu X, Christendat D. Structural insight on the mechanism of regulation of the MarR family of proteins: high-resolution crystal structure of a transcriptional repressor from Methanobacterium thermoautotrophicum. J Mol Biol 2008; 377: 655-667.
22. Perera IC, Lee YH, Wilkinson SP, Grove A. Mechanism for attenuation of DNA binding by MarR family transcriptional regulators by small molecule ligands. J Mol Biol 2009; 390: 1019-1029.