Single-Stranded DNA-Binding Protein Complex from Helicobacter pylori Suggests an ssDNA-Binding Surface

Journal of Molecular Biology

Volumn 388, Issue 3, 2009, Pages 508-519

  Chan, Kun Wei ^a   Lee, Yi Juan ^a   Wang, Chia Hung ^a   Huang, Haimei ^a   Sun, Yuh Ju ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

binding surface; Helicobacter pylori; oligonucleotide oligosaccharide binding fold; single stranded DNA; single stranded DNA binding protein

Indexed keywords

DNA BINDING PROTEIN; OLIGONUCLEOTIDE; OLIGOSACCHARIDE; SINGLE STRANDED DNA; TRYPTOPHAN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; DNA BINDING; FLUORESCENCE ANALYSIS; GEL MOBILITY SHIFT ASSAY; HELICOBACTER PYLORI; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION;

HELICOBACTER PYLORI;

EID: 64649099756     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.03.022     Document Type: Article

References (50)

1. Chase J.W., and Williams K.R. Single-stranded DNA binding proteins required for DNA replication. Annu. Rev. Biochem. 55 (1986) 103-136
2. Lohman T.M., and Ferrari M.E. Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu. Rev. Biochem. 63 (1994) 527-570
3. Meyer R.R., and Laine P.S. The single-stranded DNA-binding protein of Escherichia coli. Microbiol. Rev. 54 (1990) 342-380
4. Murzin A.G. OB (oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12 (1993) 861-867
5. Arcus V. OB-fold domains: a snapshot of the evolution of sequence, structure and function. Curr. Opin. Struct. Biol. 12 (2002) 794-801
6. Venclovas C., Ginalski K., and Kang C. Sequence-structure mapping errors in the PDB: OB-fold domains. Protein Sci. 13 (2004) 1594-1602
7. Genschel J., Curth U., and Urbanke C. Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy-terminus of SSB is the recognition site for the nuclease. Biol. Chem. 381 (2000) 183-192
8. Handa P., Acharya N., and Varshney U. Chimeras between single-stranded DNA-binding proteins from Escherichia coli and Mycobacterium tuberculosis reveal that their C-terminal domains interact with uracil DNA glycosylases. J. Biol. Chem. 276 (2001) 16992-16997
9. Reddy M.S., Guhan N., and Muniyappa K. Characterization of single-stranded DNA-binding proteins from Mycobacteria. The carboxyl-terminal of domain of SSB is essential for stable association with its cognate RecA protein. J. Biol. Chem. 276 (2001) 45959-45968
10. Kinebuchi T., Shindo H., Nagai H., Shimamoto N., and Shimizu M. Functional domains of Escherichia coli single-stranded DNA binding protein as assessed by analyses of the deletion mutants. Biochemistry 36 (1997) 6732-6738
11. Savvides S.N., Raghunathan S., Futterer K., Kozlov A.G., Lohman T.M., and Waksman G. The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA. Protein Sci. 13 (2004) 1942-1947
12. Yang C., Curth U., Urbanke C., and Kang C. Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution. Nat. Struct. Biol. 4 (1997) 153-157
13. Dabrowski S., Olszewski M., Piatek R., Brillowska-Dabrowska A., Konopa G., and Kur J. Identification and characterization of single-stranded DNA-binding proteins from Thermus thermophilus and Thermus aquaticus-new arrangement of binding domains. Microbiology 148 (2002) 3307-3315
14. Eggington J.M., Haruta N., Wood E.A., and Cox M.M. The single-stranded DNA-binding protein of Deinococcus radiodurans. BMC Microbiol. 4 (2004) 2-14
15. Witte G., Urbanke C., and Curth U. Single-stranded DNA-binding protein of Deinococcus radiodurans: a biophysical characterization. Nucleic Acids Res. 33 (2005) 1662-1670
16. Bernstein D.A., Eggington J.M., Killoran M.P., Misic A.M., Cox M.M., and Keck J.L. Crystal structure of the Deinococcus radiodurans single-stranded DNA-binding protein suggests a mechanism for coping with DNA damage. Proc. Natl Acad. Sci. USA 101 (2004) 8575-8580
17. Kerr I.D., Wadsworth R.I., Cubeddu L., Blankenfeldt W., Naismith J.H., and White M.F. Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J. 22 (2003) 2561-2570
18. Bujalowski W., and Lohman T.M. Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA. Biochemistry 25 (1986) 7799-7802
19. Hatch K., Danilowicz C., Coljee V., and Prentiss M. Measurement of the salt-dependent stabilization of partially open DNA by Escherichia coli SSB protein. Nucleic Acids Res. 36 (2008) 294-299
20. Roy R., Kozlov A.G., Lohman T.M., and Ha T. Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein. J. Mol. Biol. 369 (2007) 1244-1257
21. Acharya N., and Varshney U. Biochemical properties of single-stranded DNA-binding protein from Mycobacterium smegmatis, a fast-growing mycobacterium and its physical and functional interaction with uracil DNA glycosylases. J. Mol. Biol. 318 (2002) 1251-1264
22. Cadman C.J., and McGlynn P. PriA helicase and SSB interact physically and functionally. Nucleic Acids Res. 32 (2004) 6378-6387
23. Morimatsu K., and Kowalczykowski S.C. RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair. Mol. Cell 11 (2003) 1337-1347
24. Han E.S., Cooper D.L., Persky N.S., Sutera Jr. V.A., Whitaker R.D., Montello M.L., and Lovett S.T. RecJ exonuclease: substrates, products and interaction with SSB. Nucleic Acids Res. 34 (2006) 1084-1091
25. Kantake N., Madiraju M.V., Sugiyama T., and Kowalczykowski S.C. Escherichia coli RecO protein anneals ssDNA complexed with its cognate ssDNA-binding protein: a common step in genetic recombination. Proc. Natl Acad. Sci. USA 99 (2002) 15327-15332
26. Hegde S.P., Qin M.H., Li X.H., Atkinson M.A., Clark A.J., Rajagopalan M., and Madiraju M.V. Interactions of RecF protein with RecO, RecR, and single-stranded DNA binding proteins reveal roles for the RecF-RecO-RecR complex in DNA repair and recombination. Proc. Natl Acad. Sci. USA 93 (1996) 14468-14473
27. Shereda R.D., Bernstein D.A., and Keck J.L. A central role for SSB in Escherichia coli RecQ DNA helicase function. J. Biol. Chem. 282 (2007) 19247-19258
28. Richard D.J., Bell S.D., and White M.F. Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase. Nucleic Acids Res. 32 (2004) 1065-1074
29. Gulbis J.M., Kazmirski S.L., Finkelstein J., Kelman Z., O'Donnell M., and Kuriyan J. Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex. Eur. J. Biochem. 271 (2004) 439-449
30. Witte G., Urbanke C., and Curth U. DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery. Nucleic Acids Res. 31 (2003) 4434-4440
31. Raghunathan S., Ricard C.S., Lohman T.M., and Waksman G. 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-Å resolution. Proc. Natl Acad. Sci. USA 94 (1997) 6652-6657
32. Saikrishnan K., Jeyakanthan J., Venkatesh J., Acharya N., Sekar K., Varshney U., and Vijayan M. Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications. J. Mol. Biol. 331 (2003) 385-393
33. Saikrishnan K., Manjunath G.P., Singh P., Jeyakanthan J., Dauter Z., Sekar K., et al. Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologous SSBs: biological implications of structural plasticity and variability in quaternary association. Acta Crystallogr., Sect. D: Biol. Crystallogr. 61 (2005) 1140-1148
34. Fedorov R., Witte G., Urbanke C., Manstein D.J., and Curth U. 3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins. Nucleic Acids Res. 34 (2006) 6708-6717
35. DiDonato M., Krishna S.S., Schwarzenbacher R., McMullan D., Jaroszewski L., Miller M.D., et al. Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution. Proteins 63 (2006) 256-260
36. Raghunathan S., Kozlov A.G., Lohman T.M., and Waksman G. Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol. 7 (2000) 648-652
37. Huang C.Y., Hsu C.H., Sun Y.J., Wu H.N., and Hsiao C.D. Complexed crystal structure of replication restart primosome protein PriB reveals a novel single-stranded DNA-binding mode. Nucleic Acids Res. 34 (2006) 3878-3886
38. Filipkowski P., and Kur J. Identification and properties of the Deinococcus grandis and Deinococcus proteolyticus single-stranded DNA binding proteins (SSB). Acta Biochim. Pol. 54 (2007) 79-87
39. Matsumoto T., Morimoto Y., Shibata N., Kinebuchi T., Shimamoto N., Tsukihara T., and Yasuoka N. Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-ray structure analysis. J. Biochem. 127 (2000) 329-335
40. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
41. DeLano W. PyMOL (2002), DeLano Scientific, San Carlos, CA
42. Bayer I., Fliess A., Greipel J., Urbanke C., and Maass G. Modulation of the affinity of the single-stranded DNA-binding protein of Escherichia coli (E. coli SSB) to poly(dT) by site-directed mutagenesis. Eur. J. Biochem. 179 (1989) 399-404
43. Schuck P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78 (2000) 1606-1619
44. Curth U., Greipel J., Urbanke C., and Maass G. Multiple binding modes of the single-stranded DNA binding protein from Escherichia coli as detected by tryptophan fluorescence and site-directed mutagenesis. Biochemistry 32 (1993) 2585-2591
45. Schwarz G., and Watanabe F. Thermodynamics and kinetics of co-operative protein-nucleic acid binding. I. General aspects of analysis of data. J. Mol. Biol. 163 (1983) 467-484
46. Otwinowski Z., Minor W., and Carter Jr. C.W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
47. Kantardjieff K.A., and Rupp B. Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci. 12 (2003) 1865-1871
48. Vagin A. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30 (1997) 1022-1025
49. McRee D.E. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
50. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 905-921