Home LiteratureArticle Details
PMID: 14704354 Published · epublish English Comparative Study Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Domain mapping of the Rad51 paralog protein complexes.

Nucleic acids research ·Vol. 32 ·No. 1 ·2004-00-00 ·Pages 169-78

Miller KA, Sawicka D, Barsky D, Albala JS

Abstract

The five human Rad51 paralogs are suggested to play an important role in the maintenance of genome stability through their function in DNA double-strand break repair. These proteins have been found to form two distinct complexes in vivo, Rad51B-Rad51C-Rad51D-Xrcc2 (BCDX2) and Rad51C-Xrcc3 (CX3). Based on the recent Pyrococcus furiosus Rad51 structure, we have used homology modeling to design deletion mutants of the Rad51 paralogs. The models of the human Rad51B, Rad51C, Xrcc3 and murine Rad51D (mRad51D) proteins reveal distinct N-terminal and C-terminal domains connected by a linker region. Using yeast two-hybrid and co-immunoprecipitation techniques, we have demonstrated that a fragment of Rad51B containing amino acid residues 1-75 interacts with the C-terminus and linker of Rad51C, residues 79-376, and this region of Rad51C also interacts with mRad51D and Xrcc3. We have also determined that the N-terminal domain of mRad51D, residues 4-77, binds to Xrcc2 while the C-terminal domain of mRad51D, residues 77-328, binds Rad51C. By this, we have identified the binding domains of the BCDX2 and CX3 complexes to further characterize the interaction of these proteins and propose a scheme for the three-dimensional architecture of the BCDX2 and CX3 paralog complexes.

MeSH Terms
Amino Acid Sequence Animals Binding Sites Computational Biology DNA-Binding Proteins/chemistry,genetics,metabolism Humans Macromolecular Substances Mice Models, Molecular Molecular Sequence Data Precipitin Tests Protein Binding Protein Structure, Tertiary Pyrococcus furiosus Rad51 Recombinase Sequence Alignment Sequence Deletion/genetics Sequence Homology, Amino Acid Two-Hybrid System Techniques
Chemicals
DNA-Binding Proteins Macromolecular Substances RAD51B protein, human RAD51C protein, human RAD51D protein, human Rad51d protein, mouse XRCC2 protein, human Xrcc2 protein, mouse RAD51 protein, human Rad51 Recombinase Rad51 protein, mouse
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Miller Kristi A
Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, 7000 East Avenue, L-448, Livermore, CA 94550, USA.
Sawicka Dorota
Barsky Daniel
Albala Joanna S
References (55)
55 references, click to expand
  1. Structure of the recA protein-ADP complex.
    Nature. 1992 Jan 23;355(6358):374-6 PMID: 1731253
  2. The RAD51 family member, RAD51L3, is a DNA-stimulated ATPase that forms a complex with XRCC2.
    J Biol Chem. 2000 Sep 15;275(37):29100-6 PMID: 10871607
  3. Backbone-dependent rotamer library for proteins. Application to side-chain prediction.
    J Mol Biol. 1993 Mar 20;230(2):543-74 PMID: 8464064
  4. Correction of chromosomal instability and sensitivity to diverse mutagens by a cloned cDNA of the XRCC3 DNA repair gene.
    Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6354-8 PMID: 7603995
  5. Homologous recombination and the roles of double-strand breaks.
    Trends Biochem Sci. 1995 Oct;20(10):387-91 PMID: 8533149
  6. The I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression.
    Genomics. 1996 Apr 1;33(1):151-2 PMID: 8617505
  7. Mapping the protein universe.
    Science. 1996 Aug 2;273(5275):595-603 PMID: 8662544
  8. The XRCC2 DNA repair gene: identification of a positional candidate.
    Genomics. 1997 Apr 1;41(1):84-92 PMID: 9126486
  9. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms.
    J Mol Evol. 1997 May;44(5):528-41 PMID: 9115177
  10. Yeast Rad55 and Rad57 proteins form a heterodimer that functions with replication protein A to promote DNA strand exchange by Rad51 recombinase.
    Genes Dev. 1997 May 1;11(9):1111-21 PMID: 9159392
  11. Isolation of human and mouse genes based on homology to REC2, a recombinational repair gene from the fungus Ustilago maydis.
    Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7417-22 PMID: 9207106
  12. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  13. SEALS: a system for easy analysis of lots of sequences.
    Proc Int Conf Intell Syst Mol Biol. 1997;5:333-9 PMID: 9322058
  14. RAD51 interacts with the evolutionarily conserved BRC motifs in the human breast cancer susceptibility gene brca2.
    J Biol Chem. 1997 Dec 19;272(51):31941-4 PMID: 9405383
  15. Identification of a novel human RAD51 homolog, RAD51B.
    Genomics. 1997 Dec 15;46(3):476-9 PMID: 9441753
  16. Isolation and characterization of RAD51C, a new human member of the RAD51 family of related genes.
    Nucleic Acids Res. 1998 Mar 1;26(5):1179-84 PMID: 9469824
  17. Isolation of novel human and mouse genes of the recA/RAD51 recombination-repair gene family.
    Nucleic Acids Res. 1998 Apr 1;26(7):1653-9 PMID: 9512535
  18. Identification, characterization, and genetic mapping of Rad51d, a new mouse and human RAD51/RecA-related gene.
    Genomics. 1998 Apr 1;49(1):103-11 PMID: 9570954
  19. The XRCC2 DNA repair gene from human and mouse encodes a novel member of the recA/RAD51 family.
    Nucleic Acids Res. 1998 Jul 1;26(13):3084-9 PMID: 9628903
  20. XRCC2 and XRCC3, new human Rad51-family members, promote chromosome stability and protect against DNA cross-links and other damages.
    Mol Cell. 1998 May;1(6):783-93 PMID: 9660962
  21. The N-terminal domain of the human Rad51 protein binds DNA: structure and a DNA binding surface as revealed by NMR.
    J Mol Biol. 1999 Jul 9;290(2):495-504 PMID: 10390347
  22. Comparative protein modelling by satisfaction of spatial restraints.
    J Mol Biol. 1993 Dec 5;234(3):779-815 PMID: 8254673
  23. Recognition of errors in three-dimensional structures of proteins.
    Proteins. 1993 Dec;17(4):355-62 PMID: 8108378
  24. Catalysis of ATP-dependent homologous DNA pairing and strand exchange by yeast RAD51 protein.
    Science. 1994 Aug 26;265(5176):1241-3 PMID: 8066464
  25. Crystal structure of the helicase domain from the replicative helicase-primase of bacteriophage T7.
    Cell. 1999 Oct 15;99(2):167-77 PMID: 10535735
  26. Disruption of muREC2/RAD51L1 in mice results in early embryonic lethality which can Be partially rescued in a p53(-/-) background.
    Mol Cell Biol. 1999 Dec;19(12):8686-93 PMID: 10567591
  27. The Protein Data Bank.
    Nucleic Acids Res. 2000 Jan 1;28(1):235-42 PMID: 10592235
  28. 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.
    Structure. 2000 Feb 15;8(2):123-35 PMID: 10673432
  29. Mammalian recombination-repair genes XRCC2 and XRCC3 promote correct chromosome segregation.
    Nat Cell Biol. 2000 Oct;2(10):757-61 PMID: 11025669
  30. Xrcc2 is required for genetic stability, embryonic neurogenesis and viability in mice.
    EMBO J. 2000 Dec 15;19(24):6675-85 PMID: 11118202
  31. Molecular dissection of interactions between Rad51 and members of the recombination-repair group.
    Mol Cell Biol. 2001 Feb;21(3):966-76 PMID: 11154282
  32. Chromosome instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs.
    Mol Cell Biol. 2001 Apr;21(8):2858-66 PMID: 11283264
  33. Complex formation by the human RAD51C and XRCC3 recombination repair proteins.
    Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8440-6 PMID: 11459987
  34. Identification and purification of two distinct complexes containing the five RAD51 paralogs.
    Genes Dev. 2001 Dec 15;15(24):3296-307 PMID: 11751635
  35. Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange.
    Genes Dev. 2001 Dec 15;15(24):3308-18 PMID: 11751636
  36. Comparative modeling of CASP4 target proteins: combining results of sequence search with three-dimensional structure assessment.
    Proteins. 2001;Suppl 5:47-54 PMID: 11835481
  37. Interactions involving the Rad51 paralogs Rad51C and XRCC3 in human cells.
    Nucleic Acids Res. 2002 Feb 15;30(4):1001-8 PMID: 11842112
  38. Involvement of Rad51C in two distinct protein complexes of Rad51 paralogs in human cells.
    Nucleic Acids Res. 2002 Feb 15;30(4):1009-15 PMID: 11842113
  39. RAD51C interacts with RAD51B and is central to a larger protein complex in vivo exclusive of RAD51.
    J Biol Chem. 2002 Mar 8;277(10):8406-11 PMID: 11744692
  40. Homologous pairing and ring and filament structure formation activities of the human Xrcc2*Rad51D complex.
    J Biol Chem. 2002 Apr 19;277(16):14315-20 PMID: 11834724
  41. Insights into DNA recombination from the structure of a RAD51-BRCA2 complex.
    Nature. 2002 Nov 21;420(6913):287-93 PMID: 12442171
  42. Complex formation by the human Rad51B and Rad51C DNA repair proteins and their activities in vitro.
    J Biol Chem. 2003 Jan 24;278(4):2469-78 PMID: 12427746
  43. Holliday junction binding activity of the human Rad51B protein.
    J Biol Chem. 2003 Jan 24;278(4):2767-72 PMID: 12441335
  44. Region and amino acid residues required for Rad51C binding in the human Xrcc3 protein.
    Nucleic Acids Res. 2003 Jul 15;31(14):4041-50 PMID: 12853621
  45. Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2.
    EMBO J. 2003 Sep 1;22(17):4566-76 PMID: 12941707
  46. Identification of chromatin-related protein interactions using protein microarrays.
    Proteomics. 2003 Nov;3(11):2101-7 PMID: 14595808
  47. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
    Biopolymers. 1983 Dec;22(12):2577-637 PMID: 6667333
  48. The relation between the divergence of sequence and structure in proteins.
    EMBO J. 1986 Apr;5(4):823-6 PMID: 3709526
  49. The structure of the E. coli recA protein monomer and polymer.
    Nature. 1992 Jan 23;355(6358):318-25 PMID: 1731246
  50. Midgestation lethality in mice deficient for the RecA-related gene, Rad51d/Rad51l3.
    Genesis. 2000 Mar;26(3):167-73 PMID: 10705376
  51. Large-scale comparison of protein sequence alignment algorithms with structure alignments.
    Proteins. 2000 Jul 1;40(1):6-22 PMID: 10813826
  52. Evidence for simultaneous protein interactions between human Rad51 paralogs.
    J Biol Chem. 2000 Jun 2;275(22):16443-9 PMID: 10749867
  53. The PSIPRED protein structure prediction server.
    Bioinformatics. 2000 Apr;16(4):404-5 PMID: 10869041
  54. The Rad51 paralog Rad51B promotes homologous recombinational repair.
    Mol Cell Biol. 2000 Sep;20(17):6476-82 PMID: 10938124
  55. Similarity of the yeast RAD51 filament to the bacterial RecA filament.
    Science. 1993 Mar 26;259(5103):1896-9 PMID: 8456314
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg925
Published
2004-00-00
Epub
2004-00-02
Pages
169-78
Language
English
Region
England
NLM ID
0411011
PMCID
PMC373258
Subset
IM
Grants
NCI NIH HHS · R01 CA081019 · United States
NCI NIH HHS · R55 CA081019 · United States
NCI NIH HHS · CA-81019-02 · United States
External Links
PubMed source DOI: 10.1093/nar/gkg925 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2