Functional evolution of BRCT domains from binding DNA to protein

Evolutionary Bioinformatics

Volumn 2011, Issue 7, 2011, Pages 87-97

  Sheng, Zi Zhang ^a,b   Zhao, Yu Qi ^a,b   Huang, Jing Fei ^a,c  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

BRCT domain; DNA damage response; Evolution; Superfamily

Indexed keywords

ARTICLE; BINDING SITE; BRCT DOMAIN; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA DAMAGE; EUKARYOTE EVOLUTION; GENOME ANALYSIS; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENETIC TREE CONSTRUCTION METHOD; PROTEIN DETERMINATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; STRUCTURE ANALYSIS;

ANIMALIA; EUKARYOTA;

EID: 80053585038     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S7084     Document Type: Article

References (42)

1. Rouse J, Jackson SP. Interfaces between the detection, signaling, and repair of DNA damage. Science. 2002;297:547-51.
2. Bork P, Hofmann K, Bucher P, Neuwald AF, Altschul SF, Koonin EV. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J. 1997;11:68-76.
3. Callebaut I, Mornon JP. From BRCA1 to RAP1: a widespread BRCT module closely associated with DNA repair. FEBS Lett. 1997;400:25-30.
4. Huyton T, Bates PA, Zhang XD, Sternberg MJE, Freemont PS. The BRCA1 C-terminal domain: structure and function. Mutat Res. 2000;460:319-32.
5. Zhang X, Moréra S, Bates PA, et al. Structure of an XRCC1 BRCT domain: a new protein-protein interaction module. EMBO J. 1998;17:6404-11.
6. Manke IA, Lowery DM, Nguyen A, Yaffe MB. BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science. 2003;302:636-9.
7. Yu X, Chini CC, He M, Mer G, Chen J. The BRCT domain is a phosphoprotein binding domain. Science. 2003;302:639-42.
8. Glover JNM, Williams RS, Lee MS. Interactions between BRCT repeats and phosphoproteins: tangled up in two. Trends Biochem Sci. 2004;29:579-85.
9. Joo WS, Jeffrey PD, Cantor SB, Finnin MS, Livingston DM, Pavletich NP. Structure of the 53BP1 BRCT region bound to p53 and its comparison to the Brca1 BRCT structure. Genes Dev. 2002;16:583-93.
10. Mohammad DH, Yaffe MB.14-3-3 proteins, FHA domains and BRCT domains in the DNA damage response. DNA Repair (Amst). 2009;8:1009-17.
11. Garcia V, Furuya K, Carr AM. Identification and functional analysis of Top BP1 and its homologs. DNA Repair. 2005;4:1227-39.
12. Shiozaki EN, Gu L, Yan N, Shi Y. Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide: implications for signaling. Mol Cell. 2004;14:405-12.
13. Aravind L, Walker DR, Koonin EV. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 1999;27:1223-42.
14. Williams RS, Green R, Glover JN. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Nat Struct Biol. 2001;8:838-42.
15. Derbyshire DJ, Basu BP, Serpell LC, et al. Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor. EMBO J. 2002;21:3863-72.
16. Dulic A, Bates, PA, Zhang X, et al. BRCT domain interactions in the heterodimeric DNA repair protein XRCC1-DNA ligase III. Biochemistry. 2001;40:5906-13.
17. Rodriguez M, Yu X, Chen J, Songyang Z. Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains. J Biol Chem. 2003;278:52914-8.
18. Rodriguez MC, Songyang Z. BRCT domains: phosphopeptide binding and signaling modules. Front Biosci. 2008;13:5905-15.
19. Williams RS, Lee MS, Hau DD, Glover JN. Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1. Nat Struct Mol Biol. 2004;11:519-25.
20. Kobayashi M, Figaroa F, Meeuwenoord N, Jansen LE, Siegal G. Characterization of the DNA binding and structural properties of the BRCT region of human replication factor C p140 subunit. J Biol Chem. 2006;281:4308-17.
21. Kobayashi M, Ab E, Bonvin AM, Siegal G. Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA Complex. J Biol Chem. 2010;285:10087-97.
22. Wang LK, Nair PA, Shuman S. Structure-guided mutational analysis of the OB, HhH, and BRCT domains of Escherichia coli DNA ligase. J Biol Chem. 2008;283:23343-52.
23. Wilkinson A, Smith A, Bullard D, et al. Analysis of ligation and DNA binding by Escherichia coli DNA ligase (LigA). Biochim Biophys Acta. 2005;1749:113-22.
24. Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755-63.
25. McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics. 2000;16:404-5.
26. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
27. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059-66.
28. Ronquist F, Huelsenbeck JP. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572-4.
29. Jobb G. TREEFINDER October 2008. Available at: www.treefinder.de. Accessed April 20, 2011.
30. Landau M, Mayrose I, Rosenberg Y, et al. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res. 2005;33:W299-302.
31. Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005;33: W244-8.
32. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins. 1995;23:318-26.
33. Holm L, Park J. DaliLite workbench for protein structure comparison. Bioinformatics. 1995;16:566-7.
34. Mueller GA, Moon AF, Derose EF. A comparison of BRCT domains involved in nonhomologous end-joining: introducing the solution structure of the BRCT domain of polymerase lambda. DNA Repair (Amst). 2008;7:1340-51.
35. Guo C, Sonoda E, Tang TS, et al. REV1 protein interacts with PCNA: significance of the REV1 BRCT domain in vitro and in vivo. Mol Cell. 2006;23:265-71.
36. Wood JL, Singh N, Mer G, Chen J. MCPH1 functions in an H2AX-dependent but MDC1-independent pathway in response to DNA damage. J Biol Chem. 2007;282:35416-23.
37. Eliezer Y, Argaman L, Rhie A, Doherty AJ, Goldberg M. The direct interaction between 53BP1 and MDC1 is required for the recruitment of 53BP1 to sites of damage. J Biol Chem. 2009;284:426-35.
38. Rappas M, Oliver AW, Pearl LH. Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1. Nucleic Acids Res. 2010;39:313-24.
39. Munoz IM, Jowsey PA, Toth R, Rouse J. Phospho-epitope binding by the BRCT domains of hPTIP controls multiple aspects of the cellular response to DNA damage. Nucleic Acids Res. 2007;35:5312-22.
40. Hassa PO, Hottiger MO. The diverse biological roles of mammalian PARPS, a small but powerful family of poly-ADP-ribose polymerases. Front Biosci. 2008;13:3046-82.
41. Masson M, Niedergang C, Schreiber V, Muller S, Menissier-de Murcia J, de Murcia G. XRCC1 is specifically associated with poly(ADP-ribose) polymerase and negatively regulates its activity following DNA damage. Mol Cell Biol. 1998;18:3563-71.
42. Lisby M, Barlow JH, Burgess RC, Rothstein R. Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell. 2004;118:699-713.