The structural basis of the response regulator DrRRA from Deinococcus radiodurans

Biochemical and Biophysical Research Communications

Volumn 417, Issue 4, 2012, Pages 1206-1212

  Liu, Ying ^a   Gao, Zeng Qiang ^a   She, Zhun ^a   Qu, Kun ^a   Wang, Wen Jia ^a   Shtykova, Eleonora V ^b   Xu, Jian Hua ^a   Ji, Chao Neng ^c   Dong, Yu Hui ^a  

^a INSTITUTE OF HIGH ENERGY PHYSICS   (China)

^b SHUBNIKOV INSTITUTE OF CRYSTALLOGRAPHY   (Russian Federation)

^c FUDAN UNIVERSITY   (China)

Author keywords

Crystal structure; Deinococcus radiodurans; DNA binding; Extensive interdomain interface; Response regulator; SAXS; Two component system

Indexed keywords

DNA; DRRRA PROTEIN; OUTER MEMBRANE PROTEIN REGULATOR; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; CRYSTAL STRUCTURE; DEINOCOCCUS RADIODURANS; DNA HELIX; PRIORITY JOURNAL; PROTEIN DEPHOSPHORYLATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DEINOCOCCUS; DNA; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SCATTERING, SMALL ANGLE; TRANS-ACTIVATORS; X-RAY DIFFRACTION;

DEINOCOCCUS RADIODURANS;

EID: 84862786574     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2011.12.110     Document Type: Article

References (27)

1. Wang L.Y., Xu G.Z., Hua Y.J., et al. DrRRA: a novel response regulator essential for the extreme radioresistance of D. radiodurans. Mol. Microbiol. 2008, 54:278-285.
2. Beier D., Gross R. Regulation of bacterial virulence by two-component systems. Curr. Opin. Microbiol. 2006, 9:143-152.
3. Galperin M.Y. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol. 2006, 188:4169-4182.
4. Makarova K.S., Aravind L., Daly M.J., et al. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol. Mol. Biol. Rev. 2001, 65:44-79.
5. Li Li-Qin, Liu Ying, Liu Peng, Dong Yu-Hui The solution conformation of the response regulator proteins from Deinococcus radiodurans studied by SAXS. Chin. Phys. C 2009, 33:1-4.
6. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. Mol. 1997, 276:307-326.
7. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr., Sect. D 1999, 55:849-861.
8. Terwilliger T.C. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr., Sect. D 2003, 59:38-44.
9. Langer G., Cohen S.X., Lamzin V.S., Perrakis A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protocol. 2008, 3:1171-1179.
10. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect. D 2004, 50:760-766.
11. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. Procheck: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
12. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J. Appl. Crystallogr. 2007, 40:658-674.
13. Bailey S. The CCP4 suite - programs for protein crystallography. Acta Crystallogr., Sect. D 1994, 50:760-763.
14. Konarev P.V., Volkov V.V., Svergun D.I., et al. PRIMUS - a Windows PC based system for small-angle scattering data analysis. J. Appl. Crystallogr. 2003, 36:1277-1282.
15. Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 1992, 25:495-503.
16. Svergun D.I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 1999, 76:2879-2886.
17. Svergun D.I., Petoukhov M.V., Koch M.H.J. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 2001, 80:2246-2953.
18. Petoukhov M.V., Svergun D.I. Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys. J. 2005, 89:1237-1250.
19. Svergun D.I., Barberato C., Koch M.H.J. CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 1995, 28:768-773.
20. Nowark E., Panjikar S., Konarev P., Svergun D.I., Tucker P.A. The structural basis of signal transduction for the response regulator PrrA from Mycobacterium tuberculosis. J. Biol. Chem. 2006, 281:9659-9666.
21. Friedland N., Mack T.R., Stock A.M., et al. Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation. Biochemistry 2007, 46:6733-6743.
22. Djordjevic S., Goudreau P.N., Xu Q., Stock A.M., West A.H. Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain. Proc. Natl. Acad. Sci. USA 1998, 95:1381-1386.
23. Bachhawat P., Swapna G.V.T., Montelione G.T., Stock A.M. Mechanism of activation for transcription factor PhoB suggested by different models of dimerization in the inactive and active states. Structure 2005, 13:1353-1363.
24. Cheung J., Bingman C.A., Waldburger C.D., et al. Crystal structure of a functional dimer of the PhoQ sensor domain. J. Biol. Chem. 2008, 283:13762-13770.
25. Robinson V.L., Wu T., Stock A.M. Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily. J. Bacteria 2003, 185:4186-4194.
26. Blanco A.G., Sola M., Gomis-Rüth F.X., Coll M. Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator. Structure 2002, 10:701-713.
27. Gouet P., Courcelle E., Stuart D.I., Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics 1999, 15:305-308.