Structural and SAXS analysis of the budding yeast SHU-complex proteins

FEBS Letters

Volumn 586, Issue 16, 2012, Pages 2306-2312

  She, Zhun ^a   Gao, Zeng Qiang ^a   Liu, Ying ^a   Wang, Wen Jia ^a   Liu, Guang Feng ^a   Shtykova, Eleonora V ^b   Xu, Jian Hua ^a   Dong, Yu Hui ^a  

^a INSTITUTE OF HIGH ENERGY PHYSICS   (China)

^b SHUBNIKOV INSTITUTE OF CRYSTALLOGRAPHY   (Russian Federation)

Author keywords

DNA binding; DNA repair; Paralog; Protein complex; SAXS

Indexed keywords

DNA; PROTEIN CSM2; PROTEIN PSY3; PROTEIN SHU1; PROTEIN SHU2; SACCHAROMYCES CEREVISIAE PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CRYSTAL STRUCTURE; CRYSTALLIZATION; GEL MOBILITY SHIFT ASSAY; IN VITRO STUDY; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN EXPRESSION; PROTEIN PURIFICATION; SACCHAROMYCES CEREVISIAE; SMALL ANGLE SCATTERING;

CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; DNA; FUNGAL PROTEINS; HOMOLOGOUS RECOMBINATION; MODELS, MOLECULAR; NUCLEAR PROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SCATTERING, RADIATION;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 84864284062     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.06.024     Document Type: Article

References (29)

1. E. Shor, J. Weinstein, and R. Rothstein A genetic screen for top3 suppressors in Saccharomyces cerevisiae identifies SHU1, SHU2, PSY3 and CSM2: four genes involved in error-free DNA repair Genetics 169 2005 1275 1289 (Pubitemid 40547442)
2. H.W. Mankouri, H.P. Ngo, and I.D. Hickson Shu proteins promote the formation of homologous recombination intermediates that are processed by Sgs1-Rmi1-Top3 Mol. Biol. Cell 18 2007 4062 4073 (Pubitemid 47519496)
3. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc. Natl. Acad. Sci. U.S.A. 98 2001 4569 4574 (Pubitemid 32295017)
4. L.G. Ball, K. Zhang, J.A. Cobb, C. Boone, and W. Xiao The yeast Shu complex couples error-free post-replication repair to homologous recombination Mol. Microbiol. 73 2009 89 102
5. V. Martin, C. Chahwan, H. Gao, V. Blais, J. Wohlschlegel, J.R. Yates 3rd, C.H. McGowan, and P. Russell Sws1 is a conserved regulator of homologous recombination in eukaryotic cells EMBO J. 25 2006 2564 2574 (Pubitemid 44012238)
6. K.A. Bernstein, R.J. Reid, I. Sunjevaric, K. Demuth, R.C. Burgess, and R. Rothstein The Shu complex, which contains Rad51 paralogues, promotes DNA repair through inhibition of the Srs2 anti-recombinase Mol. Biol. Cell 22 2011 1599 1607
7. J.P. Braybrooke, K.G. Spink, J. Thacker, and I.D. Hickson The RAD51 family member, RAD51L3, is a DNA-stimulated ATPase that forms a complex with XRCC2 J. Biol. Chem. 275 2000 29100 29106
8. Y.M. Kim, and B.S. Choi Structural and functional characterization of the N-terminal domain of human Rad51D Int. J. Biochem. Cell Biol. 43 2011 416 422
9. K.S. Makarova, L. Aravind, and E.V. Koonin SWIM, a novel Zn-chelating domain present in bacteria, archaea and eukaryotes Trends Biochem. Sci. 27 2002 384 386 (Pubitemid 34874743)
10. Y. Tao, X. Li, Y. Liu, J. Ruan, S. Qi, L. Niu, and M. Teng Structural analysis of Shu proteins reveals a DNA-binding role essential for resisting damage J. Biol. Chem. 2012
11. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Method Enzymol. 276 1997 307 326 (Pubitemid 27085611)
12. T.C. Terwilliger, and J. Berendzen Automated MAD and MIR structure solution Acta Crystallogr. Sect. D Biol. Crystallogr. 55 1999 849 861 (Pubitemid 29194533)
13. T.C. Terwilliger Automated main-chain model building by template matching and iterative fragment extension Acta Crystallogr. Sect. D Biol. Crystallogr. 59 2003 38 44 (Pubitemid 36117204)
14. G. Langer, S.X. Cohen, V.S. Lamzin, and A. Perrakis Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Nat. Protocols 3 2008 1171 1179
15. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.W. Hung, G.J. Kapral, R.W. Grosse-Kunstleve, A.J. McCoy, N.W. Moriarty, R. Oeffner, R.J. Read, D.C. Richardson, J.S. Richardson, T.C. Terwilliger, and P.H. Zwart PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. Sect. D Biol. Crystallogr. 66 2010 213 221
16. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. Sect. D Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
17. R.A. Laskowski, M.W. Macarthur, D.S. Moss, and J.M. Thornton Procheck - a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
18. M.W. Roessle, R. Klaering, U. Ristau, B. Robrahn, D. Jahn, T. Gehrmann, P. Konarev, A. Round, S. Fiedler, C. Hermes, and D. Svergun Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg J. Appl. Crystallogr. 40 2007 S190 S194
19. A.R. Round, D. Franke, S. Moritz, R. Huchler, M. Fritsche, D. Malthan, R. Klaering, D.I. Svergun, and M. Roessle Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33 J. Appl. Crystallogr. 41 2008 913 917
20. P.V. Konarev, V.V. Volkov, A.V. Sokolova, M.H.J. Koch, and D.I. Svergun PRIMUS: a windows PC-based system for small-angle scattering data analysis J. Appl. Crystallogr. 36 2003 1277 1282
21. D.I. Svergun Determination of the regularization parameter in indirect-transform methods using perceptual criteria J. Appl. Crystallogr. 25 1992 495 503 (Pubitemid 23564996)
22. D.I. Svergun Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing Biophys. J. 76 1999 2879 2886 (Pubitemid 29269438)
23. D.I. Svergun, M.V. Petoukhov, and M.H.J. Koch Determination of domain structure of proteins from X-ray solution scattering Biophys. J. 80 2001 2946 2953 (Pubitemid 32521666)
24. D. Svergun, C. Barberato, and M.H.J. Koch CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Crystallogr. 28 1995 768 773 (Pubitemid 3014671)
25. D.S. Shin, L. Pellegrini, D.S. Daniels, B. Yelent, L. Craig, D. Bates, D.S. Yu, M.K. Shivji, C. Hitomi, A.S. Arvai, N. Volkmann, H. Tsuruta, T.L. Blundell, A.R. Venkitaraman, and J.A. Tainer Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2 EMBO J. 22 2003 4566 4576 (Pubitemid 37087209)
26. Z. Chen, H. Yang, and N.P. Pavletich Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures Nature 453 2008 489 494 (Pubitemid 351733325)
27. J. Liu, L. Renault, X. Veaute, F. Fabre, H. Stahlberg, and W.D. Heyer Rad51 paralogues Rad55-Rad57 balance the antirecombinase Srs2 in Rad51 filament formation Nature 479 2011 245 248
28. P. Sung Yeast Rad55 and Rad57 proteins form a heterodimer that functions with replication protein A to promote DNA strand exchange by Rad51 recombinase Genes Dev. 11 1997 1111 1121 (Pubitemid 27225219)
29. H. Yokoyama, N. Sarai, W. Kagawa, R. Enomoto, T. Shibata, H. Kurumizaka, and S. Yokoyama Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex Nucleic Acids Res. 32 2004 2556 2565 (Pubitemid 38854808)