메뉴 건너뛰기




Volumn 48, Issue 10, 2009, Pages 2087-2098

The reopening rate of the fingers domain is a determinant of base selectivity for RB69 DNA polymerase

Author keywords

[No Author keywords available]

Indexed keywords

BASE SELECTIVITIES; CATALYTIC METALS; CONFORMATIONAL CHANGES; DIVALENT METAL IONS; DNA POLYMERASE; DNA POLYMERIZATIONS; METAL BINDINGS; METAL ION; NUCLEOTIDE ANALOGUES; QUENCH FLOWS; STOPPED FLOWS; TRANSFER REACTIONS; TRIPHOSPHATE;

EID: 64349098481     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi8016284     Document Type: Article
Times cited : (23)

References (30)
  • 1
    • 0025783442 scopus 로고
    • Fidelity mechanisms in DNA replication
    • Echols, H., and Goodman, M. F. (1991) Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 60, 477-511.
    • (1991) Annu. Rev. Biochem , vol.60 , pp. 477-511
    • Echols, H.1    Goodman, M.F.2
  • 2
    • 0027220197 scopus 로고
    • Conformational coupling in DNA polymerase fidelity
    • Johnson, K. A. (1993) Conformational coupling in DNA polymerase fidelity. Annu. Rev. Biochem. 62, 685-713.
    • (1993) Annu. Rev. Biochem , vol.62 , pp. 685-713
    • Johnson, K.A.1
  • 3
    • 8544278025 scopus 로고    scopus 로고
    • DNA polymerase fidelity: Kinetics, structure, and checkpoints
    • Joyce, C. M., and Benkovic, S. J. (2004) DNA polymerase fidelity: Kinetics, structure, and checkpoints. Biochemistry 43, 14317-14324.
    • (2004) Biochemistry , vol.43 , pp. 14317-14324
    • Joyce, C.M.1    Benkovic, S.J.2
  • 5
    • 36949055511 scopus 로고
    • Comparative rates of spontaneous mutation
    • Drake, J. W. (1969) Comparative rates of spontaneous mutation. Nature 221, 1132.
    • (1969) Nature , vol.221 , pp. 1132
    • Drake, J.W.1
  • 6
    • 0035997344 scopus 로고    scopus 로고
    • Error-prone repair DNA polymerases in prokaryotes and eukaryotes
    • Goodman, M. F. (2002) Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71, 17-50.
    • (2002) Annu. Rev. Biochem , vol.71 , pp. 17-50
    • Goodman, M.F.1
  • 7
    • 0026639873 scopus 로고
    • DNA replication fidelity
    • Kunkel, T. A. (1992) DNA replication fidelity. J. Biol. Chem. 267, 18251-18254.
    • (1992) J. Biol. Chem , vol.267 , pp. 18251-18254
    • Kunkel, T.A.1
  • 8
    • 2342419732 scopus 로고    scopus 로고
    • DNA replication fidelity
    • Kunkel, T. A. (2004) DNA replication fidelity. J. Biol. Chem. 279, 16895-16898.
    • (2004) J. Biol. Chem , vol.279 , pp. 16895-16898
    • Kunkel, T.A.1
  • 9
    • 0021237247 scopus 로고
    • On the fidelity of DNA replication. The accuracy of T4 DNA polymerases in copying X174 DNA in vitro
    • Kunkel, T. A., Loeb, L. A., and Goodman, M. F. (1984) On the fidelity of DNA replication. The accuracy of T4 DNA polymerases in copying X174 DNA in vitro. J. Biol. Chem. 259, 1539-1545.
    • (1984) J. Biol. Chem , vol.259 , pp. 1539-1545
    • Kunkel, T.A.1    Loeb, L.A.2    Goodman, M.F.3
  • 10
    • 0015524064 scopus 로고
    • Studies on the biochemical basis of spontaneous mutation. I. A comparison of the deoxyribonucleic acid polymerases of mutator, antimutator, and wild type strains of bacteriophage T4
    • Muzyczka, N., Poland, R. L., and Bessman, M. J. (1972) Studies on the biochemical basis of spontaneous mutation. I. A comparison of the deoxyribonucleic acid polymerases of mutator, antimutator, and wild type strains of bacteriophage T4. J. Biol. Chem. 247, 7116-7122.
    • (1972) J. Biol. Chem , vol.247 , pp. 7116-7122
    • Muzyczka, N.1    Poland, R.L.2    Bessman, M.J.3
  • 11
    • 0037183526 scopus 로고    scopus 로고
    • A reexamination of the nucleotide incorporation fidelity of DNA polymerases
    • Showalter, A. K., and Tsai, M. D. (2002) A reexamination of the nucleotide incorporation fidelity of DNA polymerases. Biochemistry 41, 10571-10576.
    • (2002) Biochemistry , vol.41 , pp. 10571-10576
    • Showalter, A.K.1    Tsai, M.D.2
  • 12
    • 0030924437 scopus 로고    scopus 로고
    • Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity
    • Goodman, M. F. (1997) Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity. Proc. Natl. Acad. Sci. U.S.A. 94, 10493-10495.
    • (1997) Proc. Natl. Acad. Sci. U.S.A , vol.94 , pp. 10493-10495
    • Goodman, M.F.1
  • 13
    • 64349100638 scopus 로고    scopus 로고
    • Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex
    • Wang, M., Lee, H., and Konigsberg, W. (2009) Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex. Biochemistry 48, 2075-2086.
    • (2009) Biochemistry , vol.48 , pp. 2075-2086
    • Wang, M.1    Lee, H.2    Konigsberg, W.3
  • 14
    • 16344376908 scopus 로고    scopus 로고
    • Use of viscogens, dNTPαS, and rhodium(III) as probes in stopped-flow experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase β
    • Bakhtina, M., Lee, S., Wang, Y., Dunlap, C., Lamarche, B., and Tsai, M. D. (2005) Use of viscogens, dNTPαS, and rhodium(III) as probes in stopped-flow experiments to obtain new evidence for the mechanism of catalysis by DNA polymerase β. Biochemistry 44, 5177-5187.
    • (2005) Biochemistry , vol.44 , pp. 5177-5187
    • Bakhtina, M.1    Lee, S.2    Wang, Y.3    Dunlap, C.4    Lamarche, B.5    Tsai, M.D.6
  • 15
    • 33644695073 scopus 로고    scopus 로고
    • Dynamics of nucleotide incorporation: Snapshots revealed by 2-aminopurine fluorescence studies
    • Hariharan, C., Bloom, L. B., Helquist, S. A., Kool, E. T., and Reha-Krantz, L. J. (2006) Dynamics of nucleotide incorporation: Snapshots revealed by 2-aminopurine fluorescence studies. Biochemistry 45, 2836-2844.
    • (2006) Biochemistry , vol.45 , pp. 2836-2844
    • Hariharan, C.1    Bloom, L.B.2    Helquist, S.A.3    Kool, E.T.4    Reha-Krantz, L.J.5
  • 16
    • 35549011905 scopus 로고    scopus 로고
    • Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/ template complexes upon binding and incorporation of matched deoxynucleoside triphosphates
    • Zhang, H., Cao, W., Zakharova, E., Konigsberg, W., and De La Cruz, E. M. (2007) Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/ template complexes upon binding and incorporation of matched deoxynucleoside triphosphates. Nucleic Acids Res. 35, 6052-6062.
    • (2007) Nucleic Acids Res , vol.35 , pp. 6052-6062
    • Zhang, H.1    Cao, W.2    Zakharova, E.3    Konigsberg, W.4    De La Cruz, E.M.5
  • 17
    • 0037343349 scopus 로고    scopus 로고
    • Computer simulation studies of the fidelity of DNA polymerases
    • Florian, J., Goodman, M. F., and Warshel, A. (2003) Computer simulation studies of the fidelity of DNA polymerases. Biopolymers 68, 286-299.
    • (2003) Biopolymers , vol.68 , pp. 286-299
    • Florian, J.1    Goodman, M.F.2    Warshel, A.3
  • 18
    • 84961974064 scopus 로고    scopus 로고
    • Computer simulation of the chemical catalysis of DNA polymerases: Discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase
    • Florian, J., Goodman, M. F., and Warshel, A. (2003) Computer simulation of the chemical catalysis of DNA polymerases: Discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase. J. Am. Chem. Soc. 125, 8163-8177.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 8163-8177
    • Florian, J.1    Goodman, M.F.2    Warshel, A.3
  • 19
    • 37349079468 scopus 로고    scopus 로고
    • Exploring the role of large conformational changes in the fidelity of DNA polymerase β
    • Xiang, Y., Goodman, M. F., Beard, W. A., Wilson, S. H., and Warshel, A. (2008) Exploring the role of large conformational changes in the fidelity of DNA polymerase β. Proteins 70, 231-247.
    • (2008) Proteins , vol.70 , pp. 231-247
    • Xiang, Y.1    Goodman, M.F.2    Beard, W.A.3    Wilson, S.H.4    Warshel, A.5
  • 20
    • 0031883128 scopus 로고    scopus 로고
    • Structural insights into DNA polymerase β fidelity: Hold tight if you want it right
    • Beard, W. A., and Wilson, S. H. (1998) Structural insights into DNA polymerase β fidelity: Hold tight if you want it right. Chem. Biol. 5, R7-R13.
    • (1998) Chem. Biol , vol.5
    • Beard, W.A.1    Wilson, S.H.2
  • 21
    • 33747462891 scopus 로고    scopus 로고
    • A new paradigm for DNA polymerase specificity
    • Tsai, Y. C., and Johnson, K. A. (2006) A new paradigm for DNA polymerase specificity. Biochemistry 45, 9675-9687.
    • (2006) Biochemistry , vol.45 , pp. 9675-9687
    • Tsai, Y.C.1    Johnson, K.A.2
  • 22
    • 0033594982 scopus 로고    scopus 로고
    • Steady-state kinetic characterization of RB69 DNA polymerase mutants that affect dNTP incorporation
    • Yang, G., Lin, T., Karam, J., and Konigsberg, W. H. (1999) Steady-state kinetic characterization of RB69 DNA polymerase mutants that affect dNTP incorporation. Biochemistry 38, 8094-8101.
    • (1999) Biochemistry , vol.38 , pp. 8094-8101
    • Yang, G.1    Lin, T.2    Karam, J.3    Konigsberg, W.H.4
  • 23
    • 2542597119 scopus 로고    scopus 로고
    • The activity of selected RB69 DNA polymerase mutants can be restored by manganese ions: The existence of alternative metal ion ligands used during the polymerization cycle
    • Zakharova, E., Wang, J., and Konigsberg, W. (2004) The activity of selected RB69 DNA polymerase mutants can be restored by manganese ions: The existence of alternative metal ion ligands used during the polymerization cycle. Biochemistry 43, 6587-6595.
    • (2004) Biochemistry , vol.43 , pp. 6587-6595
    • Zakharova, E.1    Wang, J.2    Konigsberg, W.3
  • 24
    • 0026464542 scopus 로고
    • Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4
    • Capson, T. L., Peliska, J. A., Kaboord, B. F., Frey, M. W., Lively, C., Dahlberg, M., and Benkovic, S. J. (1992) Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4. Biochemistry 31, 10984-10994.
    • (1992) Biochemistry , vol.31 , pp. 10984-10994
    • Capson, T.L.1    Peliska, J.A.2    Kaboord, B.F.3    Frey, M.W.4    Lively, C.5    Dahlberg, M.6    Benkovic, S.J.7
  • 25
    • 0000832449 scopus 로고
    • Preparation of rhodium (III) perchlorate hexahydrate
    • Ayres, G. H., and Forrester, J. S. (1957) Preparation of rhodium (III) perchlorate hexahydrate. J. Inorg. Nucl. Chem. 3, 365-366.
    • (1957) J. Inorg. Nucl. Chem , vol.3 , pp. 365-366
    • Ayres, G.H.1    Forrester, J.S.2
  • 26
    • 0026033193 scopus 로고
    • Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant
    • Patel, S. S., Wong, I., and Johnson, K. A. (1991) Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 30, 511-525.
    • (1991) Biochemistry , vol.30 , pp. 511-525
    • Patel, S.S.1    Wong, I.2    Johnson, K.A.3
  • 27
    • 33745052090 scopus 로고    scopus 로고
    • Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: Eevaluating amino acid group contribution and allosteric coupling for ionized residues in human pol β
    • Xiang, Y., Oelschlaeger, P., Florian, J., Goodman, M. F., and Warshel, A. (2006) Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: Eevaluating amino acid group contribution and allosteric coupling for ionized residues in human pol β. Biochemistry 45, 7036-7048.
    • (2006) Biochemistry , vol.45 , pp. 7036-7048
    • Xiang, Y.1    Oelschlaeger, P.2    Florian, J.3    Goodman, M.F.4    Warshel, A.5
  • 28
    • 34248370198 scopus 로고    scopus 로고
    • A unified kinetic mechanism applicable to multiple DNA polymerases
    • Bakhtina, M., Roettger, M. P., Kumar, S., and Tsai, M. D. (2007) A unified kinetic mechanism applicable to multiple DNA polymerases. Biochemistry 46, 5463-5472.
    • (2007) Biochemistry , vol.46 , pp. 5463-5472
    • Bakhtina, M.1    Roettger, M.P.2    Kumar, S.3    Tsai, M.D.4
  • 30
    • 0030760966 scopus 로고    scopus 로고
    • DNA polymerase β: Multiple conformational changes in the mechanism of catalysis
    • Zhong, X., Patel, S. S., Werneburg, B. G., and Tsai, M. D. (1997) DNA polymerase β: Multiple conformational changes in the mechanism of catalysis. Biochemistry 36, 11891-11900.
    • (1997) Biochemistry , vol.36 , pp. 11891-11900
    • Zhong, X.1    Patel, S.S.2    Werneburg, B.G.3    Tsai, M.D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.