The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes

Nature Communications

Volumn 5, Issue , 2014, Pages 1-12

  Zhao, Qi ^a   Saro, Dorina ^a   Sachpatzidis, Aristidis ^a   Singh, Thiyam Ramsing ^b   Schlingman, Daniel ^a   Zheng, Xiao Feng ^a   MacK, Andrew ^c   Tsai, Miaw Sheue ^d   Mochrie, Simon ^c   Regan, Lynne ^a   Meetei, Amom Ruhikanta ^b   Sung, Patrick ^a   Xiong, Yong ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^c Yale University   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; HISTONE; MHF PROTEIN; UNCLASSIFIED DRUG; APITD1 PROTEIN, HUMAN; APOPTOSIS REGULATORY PROTEIN; DNA; DNA BINDING PROTEIN; DNA HELICASE; FANCM PROTEIN, HUMAN; NUCLEAR PROTEIN; STRA13 PROTEIN, HUMAN; TUMOR SUPPRESSOR PROTEIN;

BIOCHEMICAL COMPOSITION; DNA; GENETIC ANALYSIS; GENOME; HOMOLOGY; PHYSIOLOGICAL RESPONSE; RECOMBINATION;

ARTICLE; CRYSTAL STRUCTURE; DNA BINDING; DNA DAMAGE; DNA STRUCTURE; FANCONI ANEMIA; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN PROCESSING; CHEMICAL STRUCTURE; DNA REPAIR; GENETICS; HUMAN; METABOLISM; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

APOPTOSIS REGULATORY PROTEINS; CRYSTALLOGRAPHY, X-RAY; DNA; DNA DAMAGE; DNA HELICASES; DNA REPAIR; DNA-BINDING PROTEINS; FANCONI ANEMIA; HUMANS; MODELS, MOLECULAR; NUCLEAR PROTEINS; PROTEIN STRUCTURE, TERTIARY; TUMOR SUPPRESSOR PROTEINS;

EID: 84891803918     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3987     Document Type: Article

References (43)

1. Auerbach, A. D. Fanconi anemia and its diagnosis. Mutat. Res. 668, 4-10 (2009).
2. Knipscheer, P. et al. The Fanconi anemia pathway promotes replicationdependent DNA interstrand cross-link repair. Science 326, 1698-1701 (2009).
3. Kashiyama, K. et al. Malfunction of nuclease ERCC1-XPF results in diverse clinical manifestations and causes Cockayne syndrome, xeroderma pigmentosum, and Fanconi anemia. Am. J. Hum. Genet. 92, 807-819 (2013).
4. Kim, H. & D'Andrea, A. D. Regulation of DNA cross-link repair by the Fanconi anemia/BRCA pathway. Genes Dev. 26, 1393-1408 (2012).
5. Kottemann, M. C. & Smogorzewska, A. Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature 493, 356-363 (2013).
6. Meetei, A. R. et al. A human ortholog of archaeal DNA repair protein Hef is defective in Fanconi anemia complementation group M. Nat. Genet. 37, 958-963 (2005). (Pubitemid 43086152)
7. Sun, W. et al. The FANCM ortholog Fml1 promotes recombination at stalled replication forks and limits crossing over during DNA double-strand break repair. Mol. Cell 32, 118-128 (2008).
8. Prakash, R. et al. Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination. Genes Dev. 23, 67-79 (2009).
9. Singh, T. R. et al. Impaired FANCD2 monoubiquitination and hypersensitivity to camptothecin uniquely characterize Fanconi anemia complementation group M. Blood 114, 174-180 (2009).
10. Gari, K., Decaillet, C., Delannoy, M., Wu, L. & Constantinou, A. Remodeling of DNA replication structures by the branch point translocase FANCM. Proc. Natl Acad. Sci. USA 105, 16107-16112 (2008).
11. Gari, K., Decaillet, C., Stasiak, A. Z., Stasiak, A. & Constantinou, A. The Fanconi anemia protein FANCM can promote branch migration of Holliday junctions and replication forks. Mol. Cell 29, 141-148 (2008).
12. Rosado, I. V., Niedzwiedz, W., Alpi, A. F. & Patel, K. J. The Walker B motif in avian FANCM is required to limit sister chromatid exchanges but is dispensable for DNA crosslink repair. Nucleic Acids Res. 37, 4360-4370 (2009).
13. Singh, T. R. et al. MHF1-MHF2, a histone-fold-containing protein complex, participates in the Fanconi anemia pathway via FANCM. Mol. Cell 37, 879-886 (2010).
14. Yan, Z. et al. A histone-fold complex and FANCM form a conserved DNAremodeling complex to maintain genome stability. Mol. Cell 37, 865-878 (2010).
15. Tao, Y. et al. The structure of the FANCM-MHF complex reveals physical features for functional assembly. Nat. Commun. 3, 782 (2012).
16. Nishino, T. et al. CENP-T-W-S-X forms a unique centromeric chromatin structure with a histone-like fold. Cell 148, 487-501 (2012).
17. Yang, H. et al. Saccharomyces cerevisiae MHF complex structurally resembles the histones (H3-H4)(2) heterotetramer and functions as a heterotetramer. Structure 20, 364-370 (2012).
18. Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355-367 (2011).
19. Schlingman, D. J., Mack, A. H., Mochrie, S. G. & Regan, L. A new method for the covalent attachment of DNA to a surface for single-molecule studies. Colloids Surf. B. Biointerfaces 83, 91-95 (2010).
20. Nowakowski, J., Shim, P. J., Prasad, G. S., Stout, C. D. & Joyce, G. F. Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme. Nat. Struct. Biol. 6, 151-156 (1999). (Pubitemid 29069778)
21. Nowakowski, J., Shim, P. J., Stout, C. D. & Joyce, G. F. Alternative conformations of a nucleic acid four-way junction. J. Mol. Biol. 300, 93-102 (2000).
22. Khuu, P. & Ho, P. S. A rare nucleotide base tautomer in the structure of an asymmetric DNA junction. Biochemistry 48, 7824-7832 (2009).
23. Duckett, D. R. et al. The structure of the Holliday junction, and its resolution. Cell 55, 79-89 (1988).
24. Murchie, A. I. H. et al. Fluorescence energy-transfer shows that the 4-way DNA junction is a right-handed cross of antiparallel molecules. Nature 341, 763-766 (1989). (Pubitemid 19260895)
25. Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y. & Morikawa, K. Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Structure 13, 143-153 (2005). (Pubitemid 40092482)
26. Chayen, N. E. The role of oil in macromolecular crystallization. Structure 5, 1269-1274 (1997). (Pubitemid 27484470)
27. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Macromol. Crystallogr. A 276, 307-326 (1997). (Pubitemid 27085611)
28. Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. A 64, 112-122 (2008).
29. Terwilliger, T. C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55, 849-861 (1999). (Pubitemid 29194533)
30. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763 (1994).
31. Cowtan, K. & Main, P. Miscellaneous algorithms for density modification. Acta Crystallogr. D Biol. Crystallogr. 54, 487-493 (1998).
32. Adams, P. D. et al. The Phenix software for automated determination of macromolecular structures. Methods 55, 94-106 (2011).
33. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132 (2004).
34. Karplus, P. A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030-1033 (2012).
35. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
36. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255 (1997). (Pubitemid 27235885)
37. Nicholls, R. A., Long, F. & Murshudov, G. N. Low-resolution refinement tools in REFMAC5. Acta Crystallogr. D Biol. Crystallogr. 68, 404-417 (2012).
38. Padilla, J. E. & Yeates, T. O. A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. Acta Crystallogr. D Biol. Crystallogr. 59, 1124-1130 (2003). (Pubitemid 36872347)
39. Jani, D. et al. Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export. Mol. Cell 33, 727-737 (2009).
40. Chook, Y. M., Lipscomb, W. N. & Ke, H. Detection and use of pseudotranslation in determination of protein structures. Acta Crystallogr. D Biol. Crystallogr. 54, 822-827 (1998). (Pubitemid 28443592)
41. Zhang, Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9 (2008).
42. Wang, M. D., Yin, H., Landick, R., Gelles, J. & Block, S. M. Stretching DNA with optical tweezers. Biophys. J. 72, 1335-1346 (1997). (Pubitemid 27113656)
43. Bloomfield, V. A. DNA condensation by multivalent cations. Biopolymers 44, 269-282 (1997).