Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site

Biochemical and Biophysical Research Communications

Volumn 326, Issue 4, 2005, Pages 766-776

  Shioi, Seijiro ^a   Ose, Toyoyuki ^b   Maenaka, Katsumi ^b   Shiroishi, Mitsunori ^b   Abe, Yoshito ^a   Kohda, Daisuke ^b   Katayama, Tsutomu ^a   Ueda, Tadashi ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

Author keywords

Primosomal protein B; Primosome; Single stranded DNA binding protein

Indexed keywords

BACTERIAL PROTEIN; MONOMER; OLIGONUCLEOTIDE; PRIMOSOMAL PROTEIN B; SINGLE STRANDED DNA; SINGLE STRANDED DNA BINDING PROTEIN; TRYPTOPHAN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; FLUORESCENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; SURFACE PLASMON RESONANCE; X RAY ANALYSIS;

AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIPROTEIN COMPLEXES; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION;

ESCHERICHIA COLI;

EID: 10644282271     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.11.104     Document Type: Article

References (50)

1. R. Schekman, J.H. Weiner, A. Weiner, and A. Kornberg Ten proteins required for conversion of phiX174 single-stranded DNA to duplex form in vitro. Resolution and reconstitution J. Biol. Chem. 250 1975 5859 5865
2. S. Wickner, and J. Hurwitz Conversion of phiX174 viral DNA to double-stranded form by purified Escherichia coli proteins Proc. Natl. Acad. Sci. USA 71 1974 4120 4124
3. K.J. Marians Enzymology of DNA in replication in prokaryotes CRC Crit. Rev. Biochem. 17 1984 153 215
4. J.Y. Ng, and K.J. Marians The ordered assembly of the phiX174-type primosome. I. Isolation and identification of intermediate protein-DNA complexes J. Biol. Chem. 271 1996 15642 15648
5. J.Y. Ng, and K.J. Marians The ordered assembly of the phiX174-type primosome. II. Preservation of primosome composition from assembly through replication J. Biol. Chem. 271 1996 15649 15655
6. M.S. Lee, and K.J. Marians The Escherichia coli primosome can translocate actively in either direction along a DNA strand J. Biol. Chem. 264 1989 14531 14542
7. K. Tougu, H. Peng, and K.J. Marians Identification of a domain of Escherichia coli primase required for functional interaction with the DnaB helicase at the replication fork J. Biol. Chem. 269 1994 4675 4682
8. K.J. Marians Prokaryotic DNA replication Annu. Rev. Biochem. 61 1992 673 719
9. H. Masai, N. Nomura, and K. Arai Roles of phi X174 type primosome- and G4 type primase-dependent primings in initiation of lagging and leading strand syntheses of DNA replication J. Biol. Chem. 265 1990 15134 15144
10. A. Kuzminov Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda Microbiol. Mol. Biol. Rev. 63 1999 751 813
11. M.M. Cox Recombinational DNA repair of damaged replication forks in Escherichia coli: questions Annu. Rev. Genet. 35 2001 53 82
12. B. Michel Replication fork arrest and DNA recombination Trends Biochem. Sci. 25 2000 173 178
13. S.J. Sandler, and K.J. Marians Role of PriA in replication fork reactivation in Escherichia coli J. Bacteriol. 182 2000 9 13
14. M.M. Cox, M.F. Goodman, K.N. Kreuzer, D.J. Sherratt, S.J. Sandler, and K.J. Marians The importance of repairing stalled replication forks Nature 404 2000 37 41
15. P. McGlynn, and R.G. Lloyd Recombinational repair and restart of damaged replication forks Nat. Rev. Mol. Cell Biol. 3 2002 859 870
16. P. McGlynn, A.A. Al-Deib, J. Liu, K.J. Marians, and R.G. Lloyd The DNA replication protein PriA and the recombination protein RecG bind D-loops J. Mol. Biol. 270 1997 212 221
17. J. Liu, and K.J. Marians PriA-directed assembly of a primosome on D loop DNA J. Biol. Chem. 274 1999 25033 25041
18. J. Liu, L. Xu, S.J. Sandler, and K.J. Marians Replication fork assembly at recombination intermediates is required for bacterial growth Proc. Natl. Acad. Sci. USA 96 1999 3552 3555
19. L. Xu, and K.J. Marians PriA mediates DNA replication pathway choice at recombination intermediates Mol. Cell 11 2003 817 826
20. G.C. Allen Jr., and A. Kornberg Assembly of the primosome of DNA replication in Escherichia coli J. Biol. Chem. 268 1993 19204 19209
21. J. Liu, P. Nurse, and K.J. Marians The ordered assembly of the phiX174-type primosome. III. PriB facilitates complex formation between PriA and DnaT J. Biol. Chem. 271 1996 15656 15661
22. D.M. LeMaster, and F.M. Richards 1H-15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type Biochemistry 24 1985 7263 7268
23. W.A. Hendrickson, J.R. Horton, and D.M. LeMaster Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure EMBO J. 9 1990 1665 1672
24. M.M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72 1976 248 254
25. B.W. Matthews Solvent content of protein crystals J. Mol. Biol. 33 1968 491 497
26. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode J.C.W. Carter R.M. Sweet Method in Enzymology 276 1997 Academic Press New York 307 326
27. G.M. Sheldrick The application of direct methods and Patterson interpretation to high-resolution native protein data Acta Crystallogr. D49 1993 18 23
28. T.C. Terwilliger, and J. Berendzen Automated structure solution for MIR and MAD Acta Crystallogr. D 55 1999 849 861
29. T.C. Terwilliger Maximum-likelihood density modification Acta. Crystallogr. D 56 2000 965 972
30. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr. 47 1991 110 119
31. T.C. Terwilliger, and J. Berendzen Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density Acta Crystallogr. D 55 1999 1872 1877
32. A. Perrakis, R. Morris, and V.S. Lamzin Automated protein model building combined with iterative structure refinement Nat. Struct. Biol. 6 1999 458 463
33. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, and G.L. Warren Crystallography and NMR system (CNS): a new software system for macromolecular structure determination Acta Crystallogr. D54 1998 905 921
34. T.M. Lohman, and L.B. Overman Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration J. Biol. Chem. 260 1985 3594 3603
35. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton A program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
36. L. Holm, and C. Sander Dali: a network tool for protein structure comparison Trends Biochem. Sci. 20 1995 478 480
37. A.G. Murzin OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences EMBO J. 12 1993 861 867
38. J. Genschel, U. Curth, and C. Urbanke 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
39. P. Handa, N. Acharya, and U. Varshney 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
40. S. Raghunathan, C.S. Ricard, T.M. Lohman, and G. Waksman 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
41. K. Purnapatre, and U. Varshney Cloning, over-expression and biochemical characterization of the single-stranded DNA binding protein from Mycobacterium tuberculosis Eur. J. Biochem. 264 1999 591 598
42. U. Curth, C. Urbanke, J. Greipel, H. Gerberding, V. Tiranti, and M. Zeviani Single-stranded-DNA-binding proteins from human mitochondria and Escherichia coli have analogous physicochemical properties Eur. J. Biochem. 221 1994 435 443
43. J.H. Weiner, L.L. Bertsch, and A. Kornberg The deoxyribonucleic acid unwinding protein of Escherichia coli. Properties and functions in replication J. Biol. Chem. 250 1975 1972 1980
44. M. Landwehr, U. Curth, and C. Urbanke A dimeric mutant of the homotetrameric single-stranded DNA binding protein from Escherichia coli Biol. Chem. 383 2002 1325 1333
45. S. Raghunathan, A.G. Kozlov, T.M. Lohman, and G. Waksman Structure of the DNA binding domain of E. coli SSB bound to ssDNA Nat. Struct. Biol. 7 2000 648 652
46. L.B. Overman, W. Bujalowski, and T.M. Lohman Equilibrium binding of Escherichia coli single-strand binding protein to single-stranded nucleic acids in the (SSB) 65 binding mode. Cation and anion effects and polynucleotide specificity Biochemistry 27 1988 456 471
47. M.M. Lopez, Katsuhide Yutani, and G.I. Makhatadze Interactions of the major cold shock protein of Bacillus subtilis CspB with single-stranded DNA templates of different base composition J. Biol. Chem. 274 1999 33601 33608
48. A.G. Kozlov, and T.M. Lohman Kinetic mechanism of direct transfer of Escherichia coli SSB tetramers between single-stranded DNA molecules Biochemistry 41 2002 11611 11627
49. M.E. Ferrari, J. Fang, and T.M. Lohman A mutation in E. coli SSB protein (W54S) alters intra-tetramer negative cooperativity and inter-tetramer positive cooperativity for single-stranded DNA binding Biophys. Chem. 64 1997 235 251
50. S.J. Hubbard, J.M. Thornton (1993), 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London