A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling

Molecular and Cellular Biology

Volumn 25, Issue 14, 2005, Pages 5880-5892

  Smith, Corey L ^a   Peterson, Craig L ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; HELICASE; PROTEIN SWI; PROTEIN SWI2; UNCLASSIFIED DRUG;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENE MUTATION; HYDROLYSIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF;

ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONSERVED SEQUENCE; DNA-BINDING PROTEINS; HISTONES; HUMANS; HYDROLYSIS; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; TRANSCRIPTION FACTORS;

SACCHAROMYCES CEREVISIAE;

EID: 21744434032     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.14.5880-5892.2005     Document Type: Article

References (35)

1. Aoyagi, S., G. Narlikar, C. Zheng, S. Sif, R. E. Kingston, and J. J. Hayes. 2002. Nucleosome remodeling by the human SWI/SNF complex requires transient global disruption of histone-DNA interactions. Mol. Cell. Biol. 22:3653-3662.
2. Boyer, L. A., C. Logic, E. Bonté, P. B. Becker, P. A. Wade, A. P. Wolffe, C. Wu, A. N. Imbalzano, and C. L. Peterson. 2000. Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes. J. Biol. Chem. 275:18864-18870.
3. 2 tetramer in nucleosome remodeling by the SWI-SNF complex. J. Biol. Chem. 275:11545-11552.
4. Caruthers, J. M., and D. B. McKay. 2002. Helicase structure and mechanism. Curr. Opin. Struct. Biol. 12:123-133.
5. Clapier, C. R., G. Langst, D. F. Corona, P. B. Becker, and K. P. Nightingale. 2001. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21:875-883.
6. Cote, J., J. Quinn, J. L. Workman, and C. L. Peterson. 1994. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265:53-60.
7. Eisen, J. A., K. S. Sweder, and P. C. Hanawalt. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23:2715-2723.
8. Fernandez, A., H. S. Guo, P. Saenz, L. Simon-Buela, M. Gomez de Cedron, and J. A. Garcia. 1997. The motif V of plum pox potyvirus CI RNA helicase is involved in NTP hydrolysis and is essential for virus RNA replication. Nucleic Acids Res. 25:4474-4480.
9. Flaus, A., and T. Owen-Hughes. 2004. Mechanisms for ATP-dependent chromatin remodelling: farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14:165-173.
10. Hall, M. C., and S. W. Matson. 1999. Helicase motifs: the engine that powers DNA unwinding. Mol. Microbiol. 34:867-877.
11. Havas, K., A. Flaus, M. Phelan, R. Kingston, P. A. Wade, D. M. J. Lilley, and T. Owen-Hughes. 2000. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 103:1133-1142.
12. Hsu, D. S., S. T. Kim, Q. Sun, and A. Sancar. 1995. Structure and function of the UvrB protein. J. Biol. Chem. 270:8319-8327.
13. Jaskelioff, M., S. Van Komen, J. E. Krebs, P. Sung, and C. L. Peterson. 2003. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J. Biol. Chem. 278:9212-9218.
14. Krebs, J. E., C. J. Fry, M. Samuels, and C. L. Peterson. 2000. Global role for chromatin remodeling enzymes in mitotic gene expression. Cell 102:587-598.
15. Laurent, B. C., I. Treich, and M. Carlson. 1993. The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. Genes Dev. 7:583-591.
16. Logic, C., and C. L. Peterson. 1999. Purification and biochemical properties of yeast SWI/SNF complex. Methods Enzymol. 304:726-741.
17. Lowary, P. T., and J. Widom. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:19-42.
18. Luger, K., T. J. Rechsteiner, and T. J. Richmond. 1999. Expression and purification of recombinant histories and nucleosome reconstitution. Methods Mol. Biol. 119:1-16.
19. Medina, P. P., J. Carretero, M. F. Fraga, M. Esteller, D. Sidransky, and M. Sanchez-Cespedes. 2004. Genetic and epigenetic screening for gene alterations of the chromatin-remodeling factor, SMARCA4/BRG1, in lung tumors. Genes Chromosomes Cancer 41:170-177.
20. Moolenaar, G. F., R. Visse, M. Ortiz-Buysse, N. Goosen, and P. van de Putte. 1994, Helicase motifs V and VI of the Escherichia coli UvrB protein of the UvrABC endonuclease are essential for the formation of the preincision complex. J. Mol. Biol. 240:294-307.
21. Muftuoglu, M., R. Selzer, J. Tuo, R. M. Brosh, Jr., and V. A. Bohr. 2002. Phenotypic consequences of mutations in the conserved motifs of the putative helicase domain of the human Cockayne syndrome group B gene. Gene 283:27-40.
22. Owen-Hughes, T., R. T. Utley, D. J. Steger, J. M. West, S. John, J. Cote, K. M. Havas, and J. L. Workman. 1999. Analysis of nucleosome disruption by ATP-driven chromatin remodeling complexes. Methods Mol. Biol. 119:319-331.
23. Peterson, C. L., and J. L. Workman. 2000. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr. Opin. Genet. Dev. 10:187-192.
24. Richmond, E., and C. L. Peterson. 1996. Functional analysis of the DNA-stimulated ATPase domain of yeast SWI2/SNF2. Nucleic Acids Res. 24:3685-3692.
25. Roberts, C. W., and S. H. Orkin. 2004. The SWI/SNF complex-chromatin and cancer. Nat. Rev. Cancer 4:133-142.
26. Sengupta, S. M., M. VanKanegan, J. Persinger, C. Logic, B. R. Cairns, C. L. Peterson, and B. Bartholomew. 2001. The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. J. Biol. Chem. 276:12636-12644.
27. Smith, C. L., R. Horowitz-Scherer, J. F. Flanagan, C. L. Woodcock, and C. L. Peterson. 2003. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol. 10:141-145.
28. Smith, C. L., and C. L. Peterson. 2004. ATP-dependent chromatin remodeling. Curr. Top. Dev. Biol. 65:115-148.
29. Thoma, N. H., B. K. Czyzewski, A. A. Alexeev, A. V. Mazin, S. C. Kowalczykowski, and N. P. Pavletich. 2005. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat. Struct. Mol. Biol. 12:350-356.
30. Velankar, S. S., P. Soultanas, M. S. Dillingham, H. S. Subramanya, and D. B. Wigley. 1999. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97:75-84.
31. Whitehouse, I., A. Flaus, B. R. Cairns, M. F. White, J. L. Workman, and T. Owen-Hughes. 1999. Nucleosome mobilization catalysed by the yeast SWI/ SNF complex. Nature 400:784-787.
32. Winston, F., and M. Carlson. 1992. Yeast SNF/SW1 transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 8:387-391.
33. Wong, A. K., F. Shanahan, Y. Chen, L. Lian, P. Ha, K. Hendricks, S. Ghaffari, D. Iliev, B. Penn, A. M. Woodland, R. Smith, G. Salada, A. Carillo, K. Laity, J. Gupte, B. Swedlund, S. V. Tavtigian, D. H. Teng, and E. Lees. 2000. BRG1, a component of the SWI-SNF complex, is mutated in multiple human tumor cell lines. Cancer Res. 60:6171-6177.
34. Yager, T. D., C. T. McMurray, and K. E, van Holde. 1989. Salt-induced release of DNA from nucleosome core particles. Biochemistry 28:2271-2281.
35. Yao, N., T. Hesson, M. Cable, Z. Hong, A. D. Kwong, H. V. Le, and P. C. Weber. 1997. Structure of the hepatitis C virus RNA helicase domain. Nat. Struct. Biol. 4:463-467.