메뉴 건너뛰기




Volumn 13, Issue 5, 2004, Pages 751-762

Snapshots of replication through an abasic lesion: Structural basis for base substitutions and frameshifts

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; DNA BASE; NUCLEOTIDE; PROTEIN DPO4; UNCLASSIFIED DRUG;

EID: 1642382214     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(04)00101-7     Document Type: Article
Times cited : (175)

References (46)
  • 2
    • 0035890599 scopus 로고    scopus 로고
    • Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): An archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic Pol η
    • Boudsocq F., Iwai S., Hanaoka F., Woodgate R. Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic Pol η Nucleic Acids Res. 29:2001;4607-4616.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 4607-4616
    • Boudsocq, F.1    Iwai, S.2    Hanaoka, F.3    Woodgate, R.4
  • 4
    • 0000449348 scopus 로고
    • Ribbon models of macromolecules
    • Carson M. Ribbon models of macromolecules. J. Mol. Graph. 5:1987;103-106.
    • (1987) J. Mol. Graph. , vol.5 , pp. 103-106
    • Carson, M.1
  • 6
    • 0032518398 scopus 로고    scopus 로고
    • Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
    • Doublie S., Tabor S., Long A.M., Richardson C.C., Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 391:1998;251-258.
    • (1998) Nature , vol.391 , pp. 251-258
    • Doublie, S.1    Tabor, S.2    Long, A.M.3    Richardson, C.C.4    Ellenberger, T.5
  • 8
    • 0035369086 scopus 로고    scopus 로고
    • Structure of the replicating complex of a Pol α family DNA polymerase
    • Franklin M.C., Wang J., Steitz T.A. Structure of the replicating complex of a Pol α family DNA polymerase. Cell. 105:2001;657-667.
    • (2001) Cell , vol.105 , pp. 657-667
    • Franklin, M.C.1    Wang, J.2    Steitz, T.A.3
  • 9
    • 0037205001 scopus 로고    scopus 로고
    • Specialized DNA polymerases, cellular survival, and the genesis of mutations
    • Friedberg E.C., Wagner R., Radman M. Specialized DNA polymerases, cellular survival, and the genesis of mutations. Science. 296:2002;1627-1630.
    • (2002) Science , vol.296 , pp. 1627-1630
    • Friedberg, E.C.1    Wagner, R.2    Radman, M.3
  • 10
    • 0036294464 scopus 로고    scopus 로고
    • Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM
    • Fromme J.C., Verdine G.L. Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM. Nat. Struct. Biol. 9:2002;544-552.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 544-552
    • Fromme, J.C.1    Verdine, G.L.2
  • 11
    • 0035997344 scopus 로고    scopus 로고
    • Error-prone repair DNA polymerases in prokaryotes and eukaryotes
    • Goodman M.F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71:2002;17-50.
    • (2002) Annu. Rev. Biochem. , vol.71 , pp. 17-50
    • Goodman, M.F.1
  • 13
    • 0037388383 scopus 로고    scopus 로고
    • Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
    • Johnson S.J., Taylor J.S., Beese L.S. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc. Natl. Acad. Sci. USA. 100:2003;3895-3900.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3895-3900
    • Johnson, S.J.1    Taylor, J.S.2    Beese, L.S.3
  • 14
    • 84889120137 scopus 로고
    • Improved methods for building models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.-Y., Cowan S.W. Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
    • (1991) Acta Crystallogr. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.-Y.2    Cowan, S.W.3
  • 15
    • 0031443646 scopus 로고    scopus 로고
    • Multiple pathways for SOS-induced mutagenesis in Escherichia coli: An overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA
    • Kim S.R., Maenhaut-Michel G., Yamada M., Yamamoto Y., Matsui K., Sofuni T., Nohmi T., Ohmori H. Multiple pathways for SOS-induced mutagenesis in Escherichia coli. an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA Proc. Natl. Acad. Sci. USA. 94:1997;13792-13797.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 13792-13797
    • Kim, S.R.1    Maenhaut-Michel, G.2    Yamada, M.3    Yamamoto, Y.4    Matsui, K.5    Sofuni, T.6    Nohmi, T.7    Ohmori, H.8
  • 16
    • 0037072865 scopus 로고    scopus 로고
    • Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment
    • Kobayashi S., Valentine M.R., Pham P., O'Donnell M., Goodman M.F. Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment. J. Biol. Chem. 277:2002;34198-34207.
    • (2002) J. Biol. Chem. , vol.277 , pp. 34198-34207
    • Kobayashi, S.1    Valentine, M.R.2    Pham, P.3    O'Donnell, M.4    Goodman, M.F.5
  • 17
    • 0037205402 scopus 로고    scopus 로고
    • Low fidelity DNA synthesis by a Y family DNA polymerase due to misalignment in the active site
    • Kokoska R.J., Bebenek K., Boudsocq F., Woodgate R., Kunkel T.A. Low fidelity DNA synthesis by a Y family DNA polymerase due to misalignment in the active site. J. Biol. Chem. 277:2002;19633-19638.
    • (2002) J. Biol. Chem. , vol.277 , pp. 19633-19638
    • Kokoska, R.J.1    Bebenek, K.2    Boudsocq, F.3    Woodgate, R.4    Kunkel, T.A.5
  • 18
    • 0347379857 scopus 로고    scopus 로고
    • The efficiency and specificity of apurinic/apyrimidinic site bypass by human DNA polymerase η and Sulfolobus solfataricus Dpo4
    • Kokoska R.J., McCulloch S.D., Kunkel T.A. The efficiency and specificity of apurinic/apyrimidinic site bypass by human DNA polymerase η and Sulfolobus solfataricus Dpo4. J. Biol. Chem. 278:2003;50537-50545.
    • (2003) J. Biol. Chem. , vol.278 , pp. 50537-50545
    • Kokoska, R.J.1    McCulloch, S.D.2    Kunkel, T.A.3
  • 20
    • 0032538337 scopus 로고    scopus 로고
    • Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: Mechanisms for nucleotide flipping and base excision
    • Lau A.Y., Scharer O.D., Samson L., Verdine G.L., Ellenberger T. Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA. mechanisms for nucleotide flipping and base excision Cell. 95:1998;249-258.
    • (1998) Cell , vol.95 , pp. 249-258
    • Lau, A.Y.1    Scharer, O.D.2    Samson, L.3    Verdine, G.L.4    Ellenberger, T.5
  • 21
    • 0032535528 scopus 로고    scopus 로고
    • Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation
    • Li Y., Korolev S., Waksman G. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I. structural basis for nucleotide incorporation EMBO J. 17:1998;7514-7525.
    • (1998) EMBO J. , vol.17 , pp. 7514-7525
    • Li, Y.1    Korolev, S.2    Waksman, G.3
  • 22
    • 0035812849 scopus 로고    scopus 로고
    • Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication
    • Ling H., Boudsocq F., Woodgate R., Yang W. Crystal structure of a Y-family DNA polymerase in action. a mechanism for error-prone and lesion-bypass replication Cell. 107:2001;91-102.
    • (2001) Cell , vol.107 , pp. 91-102
    • Ling, H.1    Boudsocq, F.2    Woodgate, R.3    Yang, W.4
  • 23
    • 0041864009 scopus 로고    scopus 로고
    • Replication of a cis-syn thymine dimer at atomic resolution
    • Ling H., Boudsocq F., Plosky B.S., Woodgate R., Yang W. Replication of a cis-syn thymine dimer at atomic resolution. Nature. 424:2003;1083-1087.
    • (2003) Nature , vol.424 , pp. 1083-1087
    • Ling, H.1    Boudsocq, F.2    Plosky, B.S.3    Woodgate, R.4    Yang, W.5
  • 25
    • 0031984807 scopus 로고    scopus 로고
    • Highly sensitive apurinic/apyrimidinic site assay can detect spontaneous and chemically induced depurination under physiological conditions
    • Nakamura J., Walker V.E., Upton P.B., Chiang S.Y., Kow Y.W., Swenberg J.A. Highly sensitive apurinic/apyrimidinic site assay can detect spontaneous and chemically induced depurination under physiological conditions. Cancer Res. 58:1998;222-225.
    • (1998) Cancer Res. , vol.58 , pp. 222-225
    • Nakamura, J.1    Walker, V.E.2    Upton, P.B.3    Chiang, S.Y.4    Kow, Y.W.5    Swenberg, J.A.6
  • 26
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and themodynamic properties of hydrocarbons
    • Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and themodynamic properties of hydrocarbons Proteins Struct. Funct. Genet. 11:1991;281-296.
    • (1991) Proteins Struct. Funct. Genet. , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 29
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 30
    • 0034734380 scopus 로고    scopus 로고
    • Lessons learned from structural results on uracil-DNA glycosylase
    • Parikh S.S., Putnam C.D., Tainer J.A. Lessons learned from structural results on uracil-DNA glycosylase. Mutat. Res. 460:2000;183-199.
    • (2000) Mutat. Res. , vol.460 , pp. 183-199
    • Parikh, S.S.1    Putnam, C.D.2    Tainer, J.A.3
  • 31
    • 0029817866 scopus 로고    scopus 로고
    • Crystal structures of human DNA polymerase β complexed with DNA: Implications for catalytic mechanism, processivity, and fidelity
    • Pelletier H., Sawaya M.R., Wolfle W., Wilson S.H., Kraut J. Crystal structures of human DNA polymerase β complexed with DNA. implications for catalytic mechanism, processivity, and fidelity Biochemistry. 35:1996;12742-12761.
    • (1996) Biochemistry , vol.35 , pp. 12742-12761
    • Pelletier, H.1    Sawaya, M.R.2    Wolfle, W.3    Wilson, S.H.4    Kraut, J.5
  • 32
    • 0037008746 scopus 로고    scopus 로고
    • The mutational specificity of the Dbh lesion bypass polymerase and its implications
    • Potapova O., Grindley N.D., Joyce C.M. The mutational specificity of the Dbh lesion bypass polymerase and its implications. J. Biol. Chem. 277:2002;28157-28166.
    • (2002) J. Biol. Chem. , vol.277 , pp. 28157-28166
    • Potapova, O.1    Grindley, N.D.2    Joyce, C.M.3
  • 34
    • 0037163036 scopus 로고    scopus 로고
    • Trans-lesion synthesis past bulky benzo[a]pyrene diol epoxide N2-dG and N6-dA lesions catalyzed by DNA bypass polymerases
    • Rechkoblit O., Zhang Y., Guo D., Wang Z., Amin S., Krzeminsky J., Louneva N., Geacintov N.E. Trans-lesion synthesis past bulky benzo[a]pyrene diol epoxide N2-dG and N6-dA lesions catalyzed by DNA bypass polymerases. J. Biol. Chem. 277:2002;30488-30494.
    • (2002) J. Biol. Chem. , vol.277 , pp. 30488-30494
    • Rechkoblit, O.1    Zhang, Y.2    Guo, D.3    Wang, Z.4    Amin, S.5    Krzeminsky, J.6    Louneva, N.7    Geacintov, N.E.8
  • 36
    • 0037085366 scopus 로고    scopus 로고
    • Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo[a]pyrene-7,8-diol 9,10-epoxide a and G adducts
    • Shen X., Sayer J.M., Kroth H., Ponten I., O'Donnell M., Woodgate R., Jerina D.M., Goodman M.F. Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo[a]pyrene-7,8-diol 9,10-epoxide A and G adducts. J. Biol. Chem. 277:2002;5265-5274.
    • (2002) J. Biol. Chem. , vol.277 , pp. 5265-5274
    • Shen, X.1    Sayer, J.M.2    Kroth, H.3    Ponten, I.4    O'Donnell, M.5    Woodgate, R.6    Jerina, D.M.7    Goodman, M.F.8
  • 37
    • 0034762679 scopus 로고    scopus 로고
    • Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus
    • Silvian L.F., Toth E.A., Pham P., Goodman M.F., Ellenberger T. Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat. Struct. Biol. 8:2001;984-989.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 984-989
    • Silvian, L.F.1    Toth, E.A.2    Pham, P.3    Goodman, M.F.4    Ellenberger, T.5
  • 38
    • 0026111317 scopus 로고
    • The 'A rule' of mutagen specificity: A consequence of DNA polymerase bypass of non-instructional lesions?
    • Strauss B.S. The 'A rule' of mutagen specificity. a consequence of DNA polymerase bypass of non-instructional lesions? Bioessays. 13:1991;79-84.
    • (1991) Bioessays , vol.13 , pp. 79-84
    • Strauss, B.S.1
  • 39
    • 0037076538 scopus 로고    scopus 로고
    • Translesion synthesis by human DNA polymerase κ on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-N(2)-BPDE (7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene)
    • Suzuki N., Ohashi E., Kolbanovskiy A., Geacintov N.E., Grollman A.P., Ohmori H., Shibutani S. Translesion synthesis by human DNA polymerase κ on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-N(2)-BPDE (7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene). Biochemistry. 41:2002;6100-6106.
    • (2002) Biochemistry , vol.41 , pp. 6100-6106
    • Suzuki, N.1    Ohashi, E.2    Kolbanovskiy, A.3    Geacintov, N.E.4    Grollman, A.P.5    Ohmori, H.6    Shibutani, S.7
  • 40
    • 0034720286 scopus 로고    scopus 로고
    • Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis
    • Tang M., Pham P., Shen X., Taylor J.S., O'Donnell M., Woodgate R., Goodman M.F. Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature. 404:2000;1014-1018.
    • (2000) Nature , vol.404 , pp. 1014-1018
    • Tang, M.1    Pham, P.2    Shen, X.3    Taylor, J.S.4    O'Donnell, M.5    Woodgate, R.6    Goodman, M.F.7
  • 41
    • 0034847259 scopus 로고    scopus 로고
    • Structure of the catalytic core of S. cerevisiae DNA polymerase η: Implications for translesion DNA synthesis
    • Trincao J., Johnson R.E., Escalante C.R., Prakash S., Prakash L., Aggarwal A.K. Structure of the catalytic core of S. cerevisiae DNA polymerase η implications for translesion DNA synthesis Mol. Cell. 8:2001;417-426.
    • (2001) Mol. Cell , vol.8 , pp. 417-426
    • Trincao, J.1    Johnson, R.E.2    Escalante, C.R.3    Prakash, S.4    Prakash, L.5    Aggarwal, A.K.6
  • 42
    • 0000918686 scopus 로고    scopus 로고
    • The dinB gene encodes a novel E. coli DNA polymerase, DNA Pol IV, involved in mutagenesis
    • Wagner J., Gruz P., Kim S.R., Yamada M., Matsui K., Fuchs R.P., Nohmi T. The dinB gene encodes a novel E. coli DNA polymerase, DNA Pol IV, involved in mutagenesis. Mol. Cell. 4:1999;281-286.
    • (1999) Mol. Cell , vol.4 , pp. 281-286
    • Wagner, J.1    Gruz, P.2    Kim, S.R.3    Yamada, M.4    Matsui, K.5    Fuchs, R.P.6    Nohmi, T.7
  • 43
    • 0026026192 scopus 로고
    • An induced-fit kinetic mechanism for DNA replication fidelity: Direct measurement by single-turnover kinetics
    • Wong I., Patel S.S., Johnson K.A. An induced-fit kinetic mechanism for DNA replication fidelity. direct measurement by single-turnover kinetics Biochemistry. 30:1991;526-537.
    • (1991) Biochemistry , vol.30 , pp. 526-537
    • Wong, I.1    Patel, S.S.2    Johnson, K.A.3
  • 44
    • 0033200360 scopus 로고    scopus 로고
    • A plethora of lesion-replicating DNA polymerases
    • Woodgate R. A plethora of lesion-replicating DNA polymerases. Genes Dev. 13:1999;2191-2195.
    • (1999) Genes Dev. , vol.13 , pp. 2191-2195
    • Woodgate, R.1
  • 46
    • 0034857266 scopus 로고    scopus 로고
    • Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain
    • Zhou B.L., Pata J.D., Steitz T.A. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol. Cell. 8:2001;427-437.
    • (2001) Mol. Cell , vol.8 , pp. 427-437
    • Zhou, B.L.1    Pata, J.D.2    Steitz, T.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.