Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54

Nature Structural and Molecular Biology

Volumn 12, Issue 4, 2005, Pages 350-356

  Thomä, Nicolas H ^a   Czyzewski, Bryan K ^a   Alexeev, Andrei A ^b   Mazin, Alexander V ^c   Kowalczykowski, Stephen C ^b   Pavletich, Nikola P ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; DEOXYRIBONUCLEOPROTEIN; PROTEIN SNF2; PROTEIN SWI; RAD51 PROTEIN; RAD54 PROTEIN; UNCLASSIFIED DRUG; ZEBRAFISH PROTEIN; DNA BINDING PROTEIN; HELICASE; RAD54 PROTEIN, ZEBRAFISH; SMARCA1 PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA SUPERCOILING; ENZYME ACTIVITY; EUKARYOTE; HOMOLOGOUS RECOMBINATION; HUMAN; HYDROLYSIS; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; SEQUENCE ANALYSIS; AMINO ACID SEQUENCE; ANIMAL; CELL LINE; CHEMICAL STRUCTURE; CHEMISTRY; CHROMATIN; CRYSTALLOGRAPHY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; ZEBRA FISH;

DANIO RERIO; EUKARYOTA;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; CELL LINE; CHROMATIN; CRYSTALLOGRAPHY; DNA HELICASES; DNA-BINDING PROTEINS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS; ZEBRAFISH; ZEBRAFISH PROTEINS;

EID: 18744364437     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb919     Document Type: Article

References (50)

1. Flaus, A. & Owen-Hughes, T. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14, 165-173 (2004).
2. Langst, G. & Becker, P.B. Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta 1677, 58-63 (2004).
3. Flaus, A. & Owen-Hughes, T. Mechanisms for ATP-dependent chromatin remodelling. Curr. Opin. Genet. Dev. 11, 148-154 (2001).
4. Becker, P.B. & Horz, W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247-273 (2002).
5. Davis, J.L., Kunisawa, R. & Thorner, J. A presumptive helicase (MOT1 gene product) affects gene expression and is required for viability in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 12, 1879-1892 (1992).
6. Gorbalenya, A.E. & Koonin, E.V. Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Opin. Struct. Biol. 3, 419-429 (1993).
7. Singleton, M.R. & Wigley, D.B. Modularity and specialization in superfamily 1 and 2 helicases. J. Bacteriol. 184, 1819-1826 (2002).
8. Caruthers, J.M. & McKay, D.B. Helicase structure and mechanism. Curr. Opin. Struct. Biol. 12, 123-133 (2002).
9. Eisen, J.A., Sweder, K.S. & Hanawalt, P.C. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23, 2715-2723 (1995).
10. Richmond, E. & Peterson, C.L. Functional analysis of the DNA-stimulated ATPase domain of yeast SWI2/SNF2. Nucleic Acids Res. 24, 3685-3692 (1996).
11. Bork, P. & Koonin, E.V. An expanding family of helicases within the 'DEAD/H' superfamily. Nucleic Acids Res. 21, 751-752 (1993).
12. Cote, J., Quinn, J., Workman, J.L. & Peterson, C.L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265, 53-60 (1994).
13. Havas, K. et al. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 103, 1133-1142 (2000).
14. Krogh, B.O. & Symington, L.S. Recombination proteins in yeast. Annu. Rev. Genet. 38, 233-271 (2004).
15. Wolner, B., van Komen, S., Sung, P. & Peterson, C.L. Recruitment of the recombinational repair machinery to a DNA double-strand break in yeast. Mol. Cell 12, 221-232 (2003).
16. Mazin, A.V., Alexeev, A.A. & Kowalczykowski, S.C. A novel function of Rad54 protein. Stabilization of the Rad51 nucleoprotein filament. J. Biol. Chem. 278, 14029-14036 (2003).
17. Alexiadis, V. & Kadonaga, J.T. Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 16, 2767-2771 (2002).
18. Alexeev, A., Mazin, A. & Kowalczykowski, S.C. Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat. Struct. Biol. 10, 182-186 (2003).
19. Jaskelioff, M., Van Komen, S., Krebs, J.E., Sung, P. & Peterson, C.L. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J. Biol. Chem. 278, 9212-9218 (2003).
20. Solinger, J.A., Kiianitsa, K. & Heyer, W.D. Rad54, a Swi2/Snf2-like recombinational repair protein, disassembles Rad51:dsDNA filaments. Mol. Cell 10, 1175-1188 (2002).
21. Van Komen, S., Petukhova, G., Sigurdsson, S., Stratton, S. & Sung, P. Superhelicity-driven homologous DNA pairing by yeast recombination factors Rad51 and Rad54. Mol. Cell 6, 563-572 (2000).
22. Tan, T.L., Kanaar, R. & Wyman, C. Rad54, a Jack of all trades in homologous recombination. DNA Repair (Amst.) 2, 787-794 (2003).
23. Petukhova, G., Stratton, S. & Sung, P. Catalysis of homologous DNA pairing by yeast Rad51 and Rad54 proteins. Nature 393, 91-94 (1998).
24. Golub, E.I., Kovalenko, O.V., Gupta, R.C., Ward, D.C. & Radding, C.M. Interaction of human recombination proteins Rad51 and Rad54. Nucleic Acids Res. 25, 4106-4110 (1997).
25. Raschle, M., Van Komen, S., Chi, P., Ellenberger, T. & Sung, P. Multiple interactions with the Rad51 recombinase govern the homologous recombination function of Rad54. J. Biol. Chem. 279, 51973-51980 (2004).
26. Alexiadis, V., Lusser, A. & Kadonaga, J.T. A conserved N-terminal motif in Rad54 is important for chromatin remodeling and homologous strand pairing. J. Biol. Chem. 279, 27824-27829 (2004).
27. Holm, L. & Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138 (1993).
28. Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256-2268 (2004).
29. Singleton, M.R., Scaife, S. & Wigley, D.B. Structural analysis of DNA replication fork reversal by RecG. Cell 107, 79-89 (2001).
30. Caruthers, J.M., Johnson, E.R. & McKay, D.B. Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase. Proc. Natl Acad. Sci. USA 97, 13080-13085 (2000).
31. Story, R.M., Li, H. & Abelson, J.N. Crystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii. Proc. Natl. Acad. Sci. USA 98, 1465-1470 (2001).
32. Bernstein, D.A., Zittel, M.C. & Keck, J.L. High-resolution structure of the E. coli RecQ helicase catalytic core. EMBO J. 22, 4910-4921 (2003).
33. Machius, M., Henry, L., Palnitkar, M. & Deisenhofer, J. Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus. Proc. Natl. Acad. Sci. USA 96, 11717-11722 (1999).
34. Kim, J.L. et al. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure 6, 89-100 (1998).
35. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 30, 276-280 (2002).
36. Velankar, S.S., Soultanas, P., Dillingham, M.S., Subramanya, H.S. & Wigley, D.B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97, 75-84 (1999).
37. Tuteja, N. & Tuteja, R. Unraveling DNA helicases. Motif, structure, mechanism and function. Eur. J. Biochem. 271, 1849-1863 (2004).
38. Boerkoel, C.F. et al. Mutant chromatin remodeling protein SMARCAL1 causes Schimke immuno-osseous dysplasia. Nat. Genet. 30, 215-220 (2002).
39. Hiramoto, T. et al. Mutations of a novel human RAD54 homologue, RAD54B, in primary cancer. Oncogene 18, 3422-3426 (1999).
40. Smirnova, M., Van Komen, S., Sung, P. & Klein, H.L. Effects of tumor-associated mutations on Rad54 functions. J. Biol. Chem. 279, 24081-24088 (2004).
41. Matsuda, M. et al. Mutations in the RAD54 recombination gene in primary cancers. Oncogene 18, 3427-3430 (1999).
42. Wada, T., Kubota, T., Fukushima, Y. & Saitoh, S. Molecular genetic study of Japanese patients with X-linked alpha-thalassemia/mental retardation syndrome (ATR-X). Am. J. Med. Genet. 94, 242-248 (2000).
43. Ristic, D., Wyman, C., Paulusma, C. & Kanaar, R. The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA. Proc. Natl. Acad. Sci. USA 98, 8454-8460 (2001).
44. Smith, C.L., Horowitz-Scherer, R., Flanagan, J.F., Woodcock, C.L. & Peterson, C.L. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol. 10, 141-145 (2003).
45. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
46. Schneider, T.R. & Sheldrick, G.M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772-1779 (2002).
47. Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M. & Paciorek, W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr. D 59, 2023-2030 (2003).
48. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
49. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
50. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).