Domain mapping of the Rad51 paralog protein complexes

Nucleic Acids Research

Volumn 32, Issue 1, 2004, Pages 169-178

  Miller, Kristi A ^a   Sawicka, Dorota ^a   Barsky, Daniel ^a   Albala, Joanna S ^a  

^a LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; ISOPROTEIN; RAD51 PROTEIN; DNA BINDING PROTEIN; RAD51 PROTEIN, HUMAN; RAD51 PROTEIN, MOUSE; RAD51C PROTEIN, HUMAN; RAD51L1 PROTEIN, HUMAN; RAD51L3 PROTEIN, HUMAN; RAD51L3 PROTEIN, MOUSE; XRCC2 PROTEIN, HUMAN; XRCC2 PROTEIN, MOUSE;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; CONTROLLED STUDY; DELETION MUTANT; DNA REPAIR; DNA STRAND BREAKAGE; GENE FUNCTION; GENE MAPPING; GENETIC STABILITY; HUMAN; IMMUNOPRECIPITATION; IN VIVO STUDY; MOUSE; NONHUMAN; PARALOGY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PYROCOCCUS FURIOSUS; SEQUENCE HOMOLOGY; TWO HYBRID SYSTEM; YEAST; AMINO ACID SEQUENCE; ANIMAL; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; GENE DELETION; GENETICS; MACROMOLECULE; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SERODIAGNOSIS;

MURINAE; PYROCOCCUS FURIOSUS;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; HUMANS; MACROMOLECULAR SUBSTANCES; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PRECIPITIN TESTS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PYROCOCCUS FURIOSUS; RAD51 RECOMBINASE; SEQUENCE ALIGNMENT; SEQUENCE DELETION; SEQUENCE HOMOLOGY, AMINO ACID; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 1242275403     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg925     Document Type: Article

References (57)

1. Shinohara,A. and Ogawa,T. (1995) Homologous recombination and the roles of double-strand breaks. Trends Biochem. Sci., 20, 387-391.
2. Sung,P. (1994) Catalysis of ATP-dependent homologous DNA pairing and strand exchange by yeast RAD51 protein. Science, 265, 1241-1243.
3. Sung,P. (1997) 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, 1111-1121.
4. Ogawa,T., Yu,X., Shinohara,A. and Egelman,E.H. (1993) Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science, 259, 1896-1899.
5. Pittman,D.L., Weinberg,L.R. and Schimenti,J.C. (1998) Identification, characterization and genetic mapping of Rad51d, a new mouse and human RAD51/RecA-related gene. Genomics, 49, 103-111.
6. Dosanjh,M.K., Collins,D.W., Fan,W., Lennon,G.G., Albala,J.S., Shen,Z. and Schild,D. (1998) Isolation and characterization of RAD51C, a new human member of the RAD51 family of related genes. Nucleic Acids Res., 26, 1179-1184.
7. Cartwright,R., Tambini,C.E., Simpson,P.J. and Thacker,J. (1998) The XRCC2 DNA repair gene from human and mouse encodes a novel member of the recA/RAD51 family. Nucleic Acids Res., 26, 3084-3089.
8. Albala,J.S., Thelen,M.P., Prange,C., Fan,W., Christensen,M., Thompson,L.H. and Lennon,G.G. (1997) Identification of a novel human RAD51 homolog, RAD51B. Genomics, 46, 476-479.
9. Rice,M.C., Smith,S.T., Bullrich,F., Havre,P. and Kmiec,E.B. (1997) Isolation of human and mouse genes based on homology to REC2, a recombinational repair gene from the fungus Ustilago maydis. Proc. Natl Acad. Sci. USA, 94, 7417-7422.
10. Liu,N., Lamerdin,J.E., Tebbs,R.S., Schild,D., Tucker,J.D., Shen,M.R., Brookman,K.W., Siciliano,M.J., Walter,C.A., Fan,W. et al. (1998) XRCC2 and XRCC3, new human Rad51-family members, promote chromosome stability and protect against DNA cross-links and other damages. Mol. Cell, 1, 783-793.
11. Tambini,C.E., George,A.M., Rommens,J.M., Tsui,L.C., Scherer,S.W. and Thacker,J. (1997) The XRCC2 DNA repair gene: identification of a positional candidate. Genomics, 41, 84-92.
12. Tebbs,R.S., Zhao,Y., Tucker,J.D., Scheerer,J.B., Siciliano,M.J., Hwang,M., Liu,N., Legerski,R.J. and Thompson,L.H. (1995) Correction of chromosomal instability and sensitivity to diverse mutagens by a cloned cDNA of the XRCC3 DNA repair gene. Proc. Natl Acad. Sci. USA, 92, 6354-6358.
13. Cartwright,R., Dunn,A.M., Simpson,P.J., Tambini,C.E. and Thacker,J. (1998) Isolation of novel human and mouse genes of the recA/RAD51 recombination-repair gene family. Nucleic Acids Res., 26, 1653-1659.
14. Pittman,D.L. and Schimenti,J.C. (2000) Midgestation lethality in mice deficient for the RecA-related gene. Rad51d/Rad5113. Genesis, 26, 167-173.
15. Shu,Z., Smith,S., Wang,L., Rice,M.C. and Kmiec,E.B. (1999) Disruption of muREC2/RAD51L1 in mice results in early embryonic lethality which can be partially rescued in a p53(-/-) background. Mol. Cell. Biol., 19, 8686-8693.
16. Deans,B., Griffin,C.S., Maconochie,M. and Thacker,J. (2000) Xrcc2 is required for genetic stability, embryonic neurogenesis and viability in mice. EMBO J., 19, 6675-6685.
17. Takata,M., Sasaki,M.S., Sonoda,E., Fukushima,T., Morrison,C., Albala,J.S., Swagemakers.S.M., Kanaar,R., Thompson,L.H. and Takeda,S. (2000) The Rad51 paralog Rad51B promotes homologous recombinational repair. Mol. Cell. Biol., 20, 6476-6482.
18. Takata,M., Sasaki,M.S., Tachiiri,S., Fukushima,T., Sonoda,E., Schild,D., Thompson,L.H. and Takeda,S. (2001) Chromosome instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs. Mol. Cell. Biol., 21, 2858-2866.
19. Griffin,C.S., Simpson,P.J. Wilson,C.R. and Thacker,J. (2000) Mammalian recombination-repair genes XRCC2 and XRCC3 promote correct chromosome segregation. Nature Cell Biol., 2, 757-761.
20. Schild,D., Lio,Y., Collins,D.W., Tsomondo,T. and Chen,D.J. (2000) Evidence for simultaneous protein interactions between human Rad51 paralogs. J. Biol. Chem., 275, 16443-16449.
21. Sigurdsson,S., Van Komen,S., Bussen,W., Schild,D., Albala,J.S. and Sung,P. (2001) Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange. Genes Dev., 15, 3308-3318.
22. Miller,K.A., Yoshikawa,D.M., McConnell,I.R., Clark,R., Schild,D. and Albala,J.S. (2002) RAD51C interacts with RAD51B and is central to a larger protein complex in vivo exclusive of RAD51. J. Biol. Chem., 277, 8406-8411.
23. Kurumizaka,H., Ikawa,S., Nakada,M., Enomoto,R., Kagawa,W., Kinebuchi,T.,Yamazoe,M., Yokoyama,S. and Shibata,T. (2002) Homologous pairing and ring and filament structure formation activities of the human Xrcc2*Rad51D complex. J. Biol. Chem., 277, 14315-14320.
24. Braybrooke,J.P., Spink,K.G., Thacker,J. and Hickson,I.D. (2000) The RAD51 family member. RAD51L3, is a DNA-stimulated ATPase that forms a complex with XRCC2. J. Biol. Chem., 275, 29100-29106.
25. Masson,J.Y., Tarsounas,M.C., Stasiak,A.Z., Stasiak,A., Shah,R., McIlwraith,M.J., Benson,F.E. and West,S.C. (2001) Identification and purification of two distinct complexes containing the five RAD51 paralogs. Genes Dev., 15, 3296-3307.
26. Wiese,C., Collins,D.W., Albala,J.S., Thompson,L.H., Kronenberg,A. and Schild,D. (2002) Interactions involving the Rad51 paralogs Rad51C and XRCC3 in human cells. Nucleic Acids Res., 30, 1001-1008.
27. Liu,N., Schild,D., Thelen,M.P. and Thompson,L.H. (2002) Involvement of Rad51C in two distinct protein complexes of Rad51 paralogs in human cells. Nucleic Acids Res., 30, 1009-1015.
28. Lio,Y.C., Mazin,A.V., Kowalczykowski,S.C. and Chen,D.J. (2003) Complex formation by the human Rad51B and Rad51C DNA repair proteins and their activities in vitro. J. Biol. Chem., 278, 2469-2478.
29. Masson,J.Y., Stasiak,A.Z., Stasiak,A., Benson,F.E. and West,S.C. (2001) Complex formation by the human RAD51C and XRCC3 recombination repair proteins. Proc. Natl Acad. Sci. USA, 98, 8440-8446.
30. Yokoyama,H., Kurumizaka,H., Ikawa,S., Yokoyama,S. and Shibata,T. (2003) Holliday junction binding activity of the human Rad51B protein. J. Biol. Chem., 278, 2767-2772.
31. Coleman,M.A., Miller,K.A., Beernink,P.T., Yoshikawa,D.M. and Albala,J.S. (2003) Identification of chromatin-related protein interactions using protein microarrays. Proteomics, 3, 2101-2107.
32. Story,R.M. and Steitz,T.A. (1992) Structure of the recA protein-ADP complex. Nature, 355, 374-376.
33. Story,R.M., Weber,I.T. and Steitz,T.A. (1992) The structure of the E. coli recA protein monomer and polymer. Nature, 355, 318-325.
34. Aihara,H., Ito,Y., Kurumizaka,H., Yokoyama,S. and Shibata,T. (1999) The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR. J. Mol. Biol., 290, 495-504.
35. Pellegrini,L., Yu,D.S., Lo,T., Anand,S., Lee,M., Blundell,T.L. and Venkitaraman,A.R. (2002) Insights into DNA recombination from the structure of a RAD51-BRCA2 complex. Nature, 420, 287-293.
36. Krejei,L., Damborsky,J., Thomsen,B., Duno,M. and Bendixen,C. (2001) Molecular dissection of interactions between Rad51 and members of the recombination-repair group. Mol. Cell. Biol., 21, 966-976.
37. Kurumizaka,H., Enomoto,R., Nakada,M., Eda,K., Yokoyama,S. and Shibata,T. (2003) Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein. Nucleic Acids Res., 31, 4041-4050.
38. Shin,D.S., Pellegrini,L., Daniels,D.S., Yelent,B., Craig,L., Bates,D., Yu,D.S., Shivji,M.K., Hitomi,C., Arvai,A.S., Volkmann,N., Tsuruta,H., Blundell,T.L., Venkitaraman,A.R. and Tainer,J.A. (2003) Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO J., 22, 4566-4576.
39. Venclovas,C. (2001) Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment. Proteins: Struct. Func. Genet., Suppl. 5, 47-54.
40. Sauder,J.M., Arthur,J.W. and Dunbrack,R.L. (2000) Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins: Struct. Func. Genet., 40, 6-22.
41. Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
42. Lennon,G., Auffray,C., Polymeropoulos,M. and Soares,M.B. (1996) The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression, Genomics, 33, 151-152.
43. Altschul,S.F., Madden,T.L. Schäffer,A.A., Zhang,J. Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
44. Walker,D.R. and Koonin,E.V. (1997) SEALS: a system for easy analysis of lots of sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 333-339.
45. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
46. McGuffin,L.J., Bryson,K. and Jones,D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
47. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
48. Sawaya,M.R., Guo,S., Tabor,S., Richardson,C.C. and Ellenberger,T. (1999) Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7. Cell, 99, 167.
49. Holm,L. and Sander,C. (1996) Mapping the protein universe. Science. 273, 595-603.
50. Dunbrack,R.L.J. and Karplus,M. (1993) Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J. Mol. Biol., 230, 543-571.
51. Sippl,M.J. (1993) Recognition of errors in 3-dimensional structures of proteins. Proteins, 17, 355-362.
52. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure - pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
53. Brendel,V., Brocchieri,L., Sandler,S.J., Clark,A.J. and Karlin,S. (1997) Evolutionary comparisons of Reca-like proteins across all major kingdoms of living organisms. J. Mol. Evol., 44, 528-541.
54. Wong,A.K.C., Pero,R., Ormonde,P.A., Tavtigian,S.V. and Bartel,P.L. (1997) RAD51 interacts with the evolutionarily conserved BRC motifs in the human breast cancer susceptibility gene brca2. J. Biol. Chem., 272, 31941-31944.
55. Kraulis,P.J. (1991) Molscript - a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
56. Merritt,E.A. and Bacon,D.J. (1997) Macromolecular Crystallography, Part B. Academic Press, San Diego, CA, Vol. 277, pp. 505-524.
57. Somoza,J.R., Menon.S., Schmidt,H., Joseph-McCarthy,D., Dessen,A., Stahl,M.L., Somers,W.S. and Sullivan,F.X. (2000) Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6-dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose. Struct. Fold. Design, 8, 123-135.