Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein a from small angle X-ray scattering

Biochemistry

Volumn 49, Issue 13, 2010, Pages 2880-2889

  Pretto, Dalyir I ^a   Tsutakawa, Susan ^c   Brosey, Chris A ^a   Castillo, Amalchi ^a   Chagot, Marie Eve ^a   Smith, Jarrod A ^a   Tainer, John A ^c   Chazin, Walter J ^a,b  

^a Center for Structural Biology   (United States)

^b VANDERBILT UNIVERSITY   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING DOMAIN; BINDING PROTEINS; BOUND STATE; DIRECT MEASUREMENT; FLEXIBLE LINKERS; GLOBULAR DOMAINS; INTER-DOMAIN; MOLECULAR DYNAMICS SIMULATIONS; MULTI DOMAINS; N-TERMINAL DOMAINS; PROTEIN INTERACTION; REPLICATION PROTEIN A; SINGLE-STRANDED DNA; SINGLE-STRANDED DNA (SS-DNA); SMALL ANGLE X-RAY SCATTERING;

DNA; GENES; MOLECULAR DYNAMICS; SCATTERING; STRUCTURAL DYNAMICS; X RAY SCATTERING;

PROTEINS;

REPLICATION FACTOR A;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; DNA BINDING; DNA STRUCTURE; GENE REPLICATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN INTERACTION; RADIATION SCATTERING; SIMULATION;

DNA, SINGLE-STRANDED; HUMANS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; REPLICATION PROTEIN A; SCATTERING, SMALL ANGLE; X-RAYS;

EUKARYOTA;

EID: 77950418698     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi9019934     Document Type: Article

References (37)

1. 1. Fanning, E., Klimovich, V., and Nager, A. R. (2006) A dynamic model for replication protein A (RPA) function in DNA processing pathways. Nucleic Acids Res. 34 (15), 4126-4137. (Pubitemid 44542191)
2. Bochkareva, E.; et al. (2002) Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA. EMBO J. 21 (7), 1855-1863.
3. 3. Bochkarev, A.; et al. (1997) Structure of the single-stranded- DNAbinding domain of replication protein A bound to DNA. Nature 385 (6612), 176-181. (Pubitemid 27034221)
4. Bochkarev, A.; et al. (1999) The crystal structure of the complex of replication protein A. subunits RP.A32 and RPA 14 reveals a mechanism for single-stranded DNA binding. EMBO J. 18 (16), 4498-4504.
5. Jacobs, D. M.; et al. (1999) Human replication protein A: Global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker. J. Biomol. NMR 14 (4), 321-331.
6. 6. Pfuetzner, R. A.; et al. (1997) Replication protein A. Characterization and crystallization of the DNA binding domain. J. Biol. Chem, 272 (1), 430-434. (Pubitemid 27021176)
7. Deng, X.; et al. (2007) Structure of the full-length human. RPA14/32 complex gives insights into the mechanism of DNA binding and. complex formation. J. Mol. Biol. 374 (4), 865-876.
8. Bochkareva, E.; et al. (2001) Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J. 20 (3), 612-618.
9. Mer, G.; et al. (2000) Structural basis for the recognition of DNA repair proteins UNG2, XPA, and RAD52 by replication factor RPA. Cell 103 (3), 449-456.
10. 10. Mer, G.; et al. (2000) Three-dimensional structure and function of replication protein A. Cold Spring Harbar Symp, Ouant, Biol. 65, 193-200. (Pubitemid 32611940)
11. Iftode, C., and Borowiec, J. A. (2000) 5'-3' molecular polarity of human replication protein A (hRPA) binding to pseudo-origin DNA substrates. Biochemistry 39 (39), 11970-11981.
12. 12. de Laat, W. L.; et al. (1998) DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev. 12 (16), 2598-2609. (Pubitemid 28406961)
13. Arunkumar, A. I.; et al. (2003) Independent and coordinated functions of replication protein A tandem high affinity singlestranded DNA binding domains. J. Biol. Chem. 278 (42), 41077-41082.
14. Binz, S. K.; et al. (2003) The phosphorylation domain of the 32-kDa subunit of replication protein A (RPA) modulates RPA-DNA interactions. Evidence for an intersubunit interaction. J. Biol. Chem. 278 (37), 35584-35591.
15. Binz, S. K., and Wold, M. S. (2008) Regulatory functions of the N-terminal domain of the 70-kDa subunit of replication protein A (RPA). J. Biol. Chem. 283 (31), 21559-21570.
16. 16. Bochkareva, E.; et al. (2005) Single-stranded. DNA mimicry in the p53 transactivation domain interaction with replication protein. A. Proc. Natl. Acad. Sci. U.S.A. 102(43), 15412-15417. (Pubitemid 41528071)
17. Ball, H. L., Myers, J. S., and. Cortez, D. (2005) ATRIP binding to replication protein A-single-stranded DNA promotes ATR-ATRIP localization but is dispensable for Chk1 phosphorylation. Mol. Biol. Cell 16 (5). 2372-2381.
18. Xu, X.; et al. (2008) The basic cleft of RPA70N binds multiple checkpoint proteins, including RAD9, to regulate ATR signaling. MoI. Cell. Biol. 28 (24), 7345-7353.
19. Daughdrill, G. W.; et al. (2001) The weak interdomain coupling observed in the 70 kDa subunit of human replication protein A. is unaffected by ssDNA binding. Nucleic Acids Res. 29 (15), 3270-3276.
20. Brosey, C. A.; et al. (2009) NMR analysis of the architecture and functional remodeling of a modular multidomain protein, RPA. J. Am. Chim. Soc. 131 (18), 6346-6347.
21. Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J., and Svergun, D. I. (2003) PRIMUS: A Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36 (Part 5), 1277-1282.
22. Svergun, D. I., Petoukhov, M. V., and Koch, M. H. (2001) Determination of domain structure of proteins from X-ray solution scattering. Rionhys. J. 80 (6), 2946-2953.
23. Pelikan, M., Hura, G. L., and Hammel, M. (2009) Structure and flexibility within proteins as identified through small angle X-ray scattering. Gen, Physiol. Biophys. 28 (2), 174-189.
24. Rohl, C. A.; et al. (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55 (3), 656-677.
25. Pettersen, E. F.; et al. (2004) UCSF Chimera: A visualization system for exploratory research and analysis. J. Commit. Chem. 25 (13), 1605-1612.
26. Hura, G. L.; et al. (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat. Methods 6 (8), 606-612.
27. Bhattacharya, S.; et al. (2002) Characterization of binding-induced changes in dynamics suggests a model for sequence-nonspecific binding of ssDNA by replication protein A. Protein Sci. 11 (10), 2316-2325.
28. Kim, C., Snyder, R. O., and Wold, M. S. (1992) Binding properties of replication protein A from human and yeast cells. Mol. Cell. Biol. 12 (7), 3050-3059.
29. Kolpashchikov, D. M.; et al. (2001) Polarity of human replication protein A binding to DNA. Nucleic Acids Res. 29 (2), 373-379.
30. Oakley, G. G.; et al. (2009) Physical interaction between replication protein A (RPA) and MRN: Involvement of RPA2 phosphorylation and the N-terminus of RPA1. Biochemistry 48 (31), 7473-7481.
31. Putnam, C. D.; et al. (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: Defining accurate macromolecular structures, conformations and assemblies in solution. O. Rey. Biophys.40 (3) 191-285.
32. Bernstein, N. K.; et al. (2009) Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, polynucleotide kinase. Nucleic Acids Res. 37 (18), 6161-6173.
33. Hammel, M.; et al. (2010) Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J. Biol. Chem, 285 (2), 1414-1423.
34. Chapados, B. R.; et al. (2004) Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116 (1), 39-50.
35. Shin, D. S.; et al. (2003) Full-length archaeal Rad51 structure and mutants: Mechanisms for RAD51 assembly and control by BRCA2. EMBO J. 22 (17), 4566-4576.
36. Williams, R. S.; et al. (2009) Nbs1 flexibly tethers Ctp1 and Mre11Rad50 to coordinate DNA double-strand break processing and repair. Cell 139 (1), 87-99.
37. Roy, R.; et al. (2009) SSB protein diffusion on single-stranded DNA stimulates RecA filament formation. Nature 461 (7267), 1092-1097.