Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein

EMBO Journal

Volumn 22, Issue 11, 2003, Pages 2561-2570

  Kerr, Iain D ^a   Wadsworth, Ross I M ^a   Cubeddu, Liza ^a   Blankenfeldt, Wulf ^b   Naismith, James H ^a   White, Malcolm F ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

Author keywords

Archaea; OB fold; Protein structure; RPA; SSB protein

Indexed keywords

BACTERIAL PROTEIN; REPLICATION PROTEIN A; SINGLE STRANDED DNA; SINGLE STRANDED DNA BINDING PROTEIN;

ARCHAEBACTERIUM; ARTICLE; CRYSTAL STRUCTURE; DNA BINDING; DNA REPLICATION; EUKARYOTE; HUMAN; INFORMATION PROCESSING; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SULFOLOBUS SOLFATARICUS; THERMODYNAMICS;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA, ARCHAEAL; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; HUMANS; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN FOLDING; RECOMBINANT PROTEINS; REPLICATION PROTEIN A; SEQUENCE HOMOLOGY, AMINO ACID; SULFOLOBUS; THERMODYNAMICS;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; SULFOLOBUS; SULFOLOBUS SOLFATARICUS;

EID: 0037526104     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg272     Document Type: Article

References (42)

1. Blackwell, L.J. and Borowiec, J.A. (1994) Human replication protein A binds single-stranded DNA in two distinct complexes. Mol. Cell. Biol., 14, 3993-4001.
2. Bochkarev, A., Pfuetzner, R.A., Edwards, M. and Frappier, L. (1997) Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature, 385, 176-181.
3. Bochkareva, E., Korolev, S. and Bochkarev, A. (2000) The role for zinc in replication protein A. J. Biol. Chem., 275, 27332-27338.
4. Bochkareva, E., Belegu, V., Korolev, S. and Bochkarev, A. (2001) Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J., 20, 612-618.
5. Bochkareva, E., Korolev, S., Lees-Miller, S.P. and Bochkarev, A. (2002) Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA. EMBO J., 21, 1855-1863.
6. Bujalowski, W. and Lohman, T.M. (1986) Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA. Biochemistry, 25, 7799-7802.
7. Chase, J.W. (1986) Single-stranded DNA binding proteins required for DNA replication. Annu. Rev. Biochem., 55, 103-136.
8. Chedin, F., Seitz, E.M. and Kowalczykowski, S.C. (1998) Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins. Trends Biochem. Sci., 23, 273-277.
9. Esnouf, R.M. (1997) An extensively modified version of MolScript that includes greatly enhanced coloring capablilities. J. Mol. Graph. Model., 15, 112-113, 132-134.
10. Evans, P.R. (1997) SCALA. Joint CCP4 and ESF-EAMCB Newsletter on Protein Crystallography, no. 33, pp. 22-24.
11. French, G.S. and Wilson, K.S. (1978) On the treatment of negative intensity observations. Acta Crystallogr. A, 34, 517-525.
12. Gomes, X.V. and Wold, M.S. (1996) Functional domains of the 70-kilodalton subunit of human replication protein A. Biochemistry, 35, 10558-10568.
13. Haseltine, C.A. and Kowalczykoski, S.C. (2002) A distinctive single-strand DNA-binding protein from the Archaeon Sulfolobus solfataricus. Mol. Microbiol., 43, 1505-1515.
14. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
15. Horvath, M.P., Schweiker, V.L., Bevilacqua, J.M., Ruggles, J.A. and Schultz, S.C. (1998) Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA. Cell, 95, 963-974.
16. Jacobs, D.M., Lipton, A.S., Isem, N.G., Daughdrill, G.W., Lowry, D.F., Gomes, X. and Wold,M.S. (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, 321-331.
17. Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A, 47, 110-119.
18. Keeling, P.J. and Doolittle, W.F. (1995) Archaea: narrowing the gap between prokaryotes and eukaryotes. Proc. Natl Acad. Sci. USA, 92, 5761-5764.
19. Kerr, I.D., Wadsworth, R.I., Blankenfeldt, W., Staines, A.G., White, M.F. and Naismith, J.H. (2001) Overexpression, purification, crystallization and data collection of a single-stranded DNA-binding protein from Sulfolobus solfataricus. Acta Crystallogr. D Biol. Crystallogr., 57, 1290-1292.
20. Kleywegt, G.J. (1996) Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D Biol. Crystallogr., 52, 842-857.
21. Kozlov, A.G. and Lohman, T.M. (1998) Calorimetric studies of E.coli SSB protein-single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy. J. Mol. Biol., 278, 999-1014.
22. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thomton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
23. Leslie, A.G.W. (1992) Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 and ESF-EAMCB Newsletter on Protein Crystallography, no. 26.
24. Lohman, T.M. and Overman, L.B. (1985) Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration. J. Biol. Chem., 260, 3594-3603.
25. Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr., 53, 240-255.
26. Murzin, A.G. (1993) OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J., 12, 861-867.
27. Perrakis, A., Morris, R. and Lamzin, V.S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol., 6, 458-463.
28. Philipova, D., Mullen, J.R., Maniar, H.S., Lu, J., Gu, C. and Brill, S.J. (1996) A-hierarchy of SSB protomers in replication protein A. Genes Dev., 10, 2222-2233.
29. Raghunathan, S., Ricard, C.S., Lohman, T.M. and Waksman,G. (1997) Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution. Proc. Natl Acad. Sci. USA, 94, 6652-6657.
30. Raghunathan, S., Kozlov, A.G., Lohman, T.M. and Waksman, G. (2000) Structure of the DNA binding domain of E.coli SSB bound to ssDNA. Nat. Struct. Biol., 7, 648-652.
31. Singleton, M.R., Scaife, S. and Wigley, D.B. (2001) Structural analysis of DNA replication fork reversal by RecG. Cell, 107, 79-89.
32. Suck, D. (1997) Common fold, common function, common origin? Nat. Struct. Biol., 4, 161-165.
33. Taylor, H.O. and Leslie, A.G.W. (1998) A program to detwin merohedrally twinned data. CCP4 Newsletter on Protein Crystallography, no. 35, p. 9.
34. Terwilliger, T.C. (2000) Maximum-likelihood density modification. Acta Crystallogr. D Biol. Crystallogr., 56, 965-972.
35. Terwilliger, T.C. and Berendzen, J. (1999) Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr., 55, 849-861.
36. VanDuyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L. and Clardy, J. (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol., 229, 105-124.
37. Vriend, G. (1990) WHAT IF: a molecular modeling and drug design program. J. Mol. Graph., 8, 52-56.
38. Wadsworth, R.I.M. and White, M.F. (2001) Identification and properties of the crenarchaeal single-stranded DNA binding protein from Sulfolobus solfataricus. Nucleic Acids Res., 29, 914-920.
39. Wold, M.S. (1997) Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem., 66, 61-92.
40. Yang, C., Curth, U., Urbanke, C. and Kang, C. (1997) Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution. Nat. Struct. Biol., 4, 153-157.
41. Yang, H. et al. (2002) BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure. Science, 297, 1837-1848.
42. Yeates, T.O. (1997) Detecting and overcoming crystal twinning. Methods Enzymol., 276, 344-358.