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Volumn 432, Issue 7016, 2004, Pages 473-478

Human DNA ligase I completely encircles and partially unwinds nicked DNA

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGENS; BIODIVERSITY; CATALYSIS; CELLS; CRYSTAL STRUCTURE; ENZYMES;

EID: 9644289536     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03082     Document Type: Article
Times cited : (279)

References (50)
  • 1
    • 0016273515 scopus 로고
    • DNA ligase: Structure, mechanism, and function
    • Lehman, I. R. DNA ligase: structure, mechanism, and function. Science 186, 790-797 (1974).
    • (1974) Science , vol.186 , pp. 790-797
    • Lehman, I.R.1
  • 2
    • 0029056990 scopus 로고
    • RNA capping enzyme and DNA ligase: A superfamily of covalent nucleotidyl transferases
    • Shuman, S. & Schwer, B. RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases. Mol. Microbiol. 17, 405-410 (1995).
    • (1995) Mol. Microbiol. , vol.17 , pp. 405-410
    • Shuman, S.1    Schwer, B.2
  • 3
    • 0026059034 scopus 로고
    • In vitro mutagenesis and functional expression in Escherichia coli of a cDNA encoding the catalytic domain of human DNA ligase I
    • Kodama, K., Barnes, D. E. & Lindahl, T. In vitro mutagenesis and functional expression in Escherichia coli of a cDNA encoding the catalytic domain of human DNA ligase I. Nucleic Acids Res. 19, 6093-6099 (1991).
    • (1991) Nucleic Acids Res. , vol.19 , pp. 6093-6099
    • Kodama, K.1    Barnes, D.E.2    Lindahl, T.3
  • 4
    • 0029744212 scopus 로고    scopus 로고
    • Identification of essential residues in Thermus thermophilus DNA ligase
    • Luo, J. & Barany, F. Identification of essential residues in Thermus thermophilus DNA ligase. Nucleic Acids Res. 24, 3079-3085 (1996).
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3079-3085
    • Luo, J.1    Barany, F.2
  • 5
    • 0032531971 scopus 로고    scopus 로고
    • Mutational analysis of Chlorella virus DNA ligase: Catalytic roles of domain I and motif VI
    • Sriskanda, V. & Shuman, S. Mutational analysis of Chlorella virus DNA ligase: catalytic roles of domain I and motif VI. Nucleic Acids Res. 26, 4618-4625 (1998).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4618-4625
    • Sriskanda, V.1    Shuman, S.2
  • 6
    • 0033618289 scopus 로고    scopus 로고
    • DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase. Identification of two functionally distinct DNA binding regions within DNA ligase III
    • Mackey, Z. B. et al. DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase. Identification of two functionally distinct DNA binding regions within DNA ligase III. J. Biol. Chem. 274, 21679-21687 (1999).
    • (1999) J. Biol. Chem. , vol.274 , pp. 21679-21687
    • Mackey, Z.B.1
  • 7
    • 0037082434 scopus 로고    scopus 로고
    • Role of nucleotidyltransferase motifs I, III and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase
    • Sriskanda, V. & Shuman, S. Role of nucleotidyltransferase motifs I, III and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase. Nucleic Acids Res. 30, 903-911 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 903-911
    • Sriskanda, V.1    Shuman, S.2
  • 8
    • 0029938467 scopus 로고    scopus 로고
    • Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7
    • Subramanya, H. S., Doherty, A. J., Ashford, S. R. & Wigley, D. B. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85, 607-615 (1996).
    • (1996) Cell , vol.85 , pp. 607-615
    • Subramanya, H.S.1    Doherty, A.J.2    Ashford, S.R.3    Wigley, D.B.4
  • 10
    • 0034161570 scopus 로고    scopus 로고
    • Crystal structure of NAD(+)-dependent DNA ligase: Modular architecture and functional implications
    • Lee, J. Y. et al. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J. 19, 1119-1129 (2000).
    • (2000) EMBO J. , vol.19 , pp. 1119-1129
    • Lee, J.Y.1
  • 11
    • 0033634655 scopus 로고    scopus 로고
    • Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining
    • Odell, M., Sriskanda, V., Shuman, S. & Nikolov, D. B. Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol. Cell 6, 1183-1193 (2000).
    • (2000) Mol. Cell , vol.6 , pp. 1183-1193
    • Odell, M.1    Sriskanda, V.2    Shuman, S.3    Nikolov, D.B.4
  • 12
    • 0034327406 scopus 로고    scopus 로고
    • Structural and mechanistic conservation in DNA ligases
    • Doherty, A. J. & Suh, S. W. Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res. 28, 4051-4058 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4051-4058
    • Doherty, A.J.1    Suh, S.W.2
  • 13
    • 0034734323 scopus 로고    scopus 로고
    • DNA ligases in the repair and replication of DNA
    • Timson, D. J., Singleton, M. R. & Wigley, D. B. DNA ligases in the repair and replication of DNA. Mutat. Res. 460, 301-318 (2000).
    • (2000) Mutat. Res. , vol.460 , pp. 301-318
    • Timson, D.J.1    Singleton, M.R.2    Wigley, D.B.3
  • 14
    • 0036231641 scopus 로고    scopus 로고
    • ATP-dependent DNA ligases
    • Reviews 3005
    • Martin, I. V. & MacNeill, S. A. ATP-dependent DNA ligases. Genome Biol. 3, Reviews 3005 (2002).
    • (2002) Genome Biol. , vol.3
    • Martin, I.V.1    MacNeill, S.A.2
  • 15
    • 0026489345 scopus 로고
    • DNA ligase I from Saccharomyces cerevisiae: Physical and biochemical characterization of the CDC9 gene product
    • Tomkinson, A. E., Tappe, N. J. & Friedberg, E. C. DNA ligase I from Saccharomyces cerevisiae: physical and biochemical characterization of the CDC9 gene product. Biochemistry 31, 11762-11771 (1992).
    • (1992) Biochemistry , vol.31 , pp. 11762-11771
    • Tomkinson, A.E.1    Tappe, N.J.2    Friedberg, E.C.3
  • 16
    • 0033570011 scopus 로고    scopus 로고
    • Mutational analysis of Escherichia coli DNA ligase identifies amino acids required for nick-ligation in vitro and for in vivo complementation of the growth of yeast cells deleted for CDC9 and LIG4
    • Sriskanda, V., Schwer, B., Ho, C. K. & Shuman, S. Mutational analysis of Escherichia coli DNA ligase identifies amino acids required for nick-ligation in vitro and for in vivo complementation of the growth of yeast cells deleted for CDC9 and LIG4. Nucleic Acids Res. 27, 3953-3963 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 3953-3963
    • Sriskanda, V.1    Schwer, B.2    Ho, C.K.3    Shuman, S.4
  • 17
    • 0032537803 scopus 로고    scopus 로고
    • DNA ligase IV binds to XRCC4 via a motif located between rather than within its BRCT domains
    • Grawunder, U., Zimmer, D. & Leiber, M. R. DNA ligase IV binds to XRCC4 via a motif located between rather than within its BRCT domains. Curr. Biol. 8, 873-876 (1998).
    • (1998) Curr. Biol. , vol.8 , pp. 873-876
    • Grawunder, U.1    Zimmer, D.2    Leiber, M.R.3
  • 18
    • 3242806042 scopus 로고    scopus 로고
    • Mutational analyses of the thermostable NAD(+)-dependent DNA ligase from Thermus filiformis
    • Jeon, H. J. et al. Mutational analyses of the thermostable NAD(+)-dependent DNA ligase from Thermus filiformis. FEMS Microbiol. Lett. 237, 111-118 (2004).
    • (2004) FEMS Microbiol. Lett. , vol.237 , pp. 111-118
    • Jeon, H.J.1
  • 20
    • 4143117765 scopus 로고    scopus 로고
    • Structural rearrangement accompanying NAD(+) synthesis within a bacterial DNA ligase crystal
    • Gajiwala, K. S. & Pinko, C. Structural rearrangement accompanying NAD(+) synthesis within a bacterial DNA ligase crystal. Structure 12, 1449-1459 (2004).
    • (2004) Structure , vol.12 , pp. 1449-1459
    • Gajiwala, K.S.1    Pinko, C.2
  • 21
    • 0038228666 scopus 로고    scopus 로고
    • X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes
    • Hakansson, K., Doherty, A. J., Shuman, S. & Wigley, D. B. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes. Cell 89, 545-553 (1997).
    • (1997) Cell , vol.89 , pp. 545-553
    • Hakansson, K.1    Doherty, A.J.2    Shuman, S.3    Wigley, D.B.4
  • 22
    • 0026680743 scopus 로고
    • Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents
    • Barnes, D. E., Tomkinson, A. E., Lehmann, A. R., Webster, A. D. & Lindahl, T. Mutations in the DNA ligase I gene of an individual with immunodeficiencies and cellular hypersensitivity to DNA-damaging agents. Cell 69, 495-503 (1992).
    • (1992) Cell , vol.69 , pp. 495-503
    • Barnes, D.E.1    Tomkinson, A.E.2    Lehmann, A.R.3    Webster, A.D.4    Lindahl, T.5
  • 23
    • 0028047308 scopus 로고
    • Aberrant DNA repair and DNA replication due to an inherited enzymatic defect in human DNA ligase I
    • Prigent, C., Satoh, M. S., Daly, G., Barnes, D. E. & Lindahl, T. Aberrant DNA repair and DNA replication due to an inherited enzymatic defect in human DNA ligase I. Mol. Cell. Biol. 14, 310-317 (1994).
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 310-317
    • Prigent, C.1    Satoh, M.S.2    Daly, G.3    Barnes, D.E.4    Lindahl, T.5
  • 24
    • 0037099729 scopus 로고    scopus 로고
    • Replication failure, genome instability, and increased cancer susceptibility in mice with a point mutation in the DNA ligase I gene
    • Harrison, C., Ketchen, A. M., Redhead, N. J., O'Sullivan, M. J. & Melton, D. W. Replication failure, genome instability, and increased cancer susceptibility in mice with a point mutation in the DNA ligase I gene. Cancer Res. 62, 4065-4074 (2002).
    • (2002) Cancer Res. , vol.62 , pp. 4065-4074
    • Harrison, C.1    Ketchen, A.M.2    Redhead, N.J.3    O'Sullivan, M.J.4    Melton, D.W.5
  • 25
    • 0032510217 scopus 로고    scopus 로고
    • The hyperthermophile chromosomal protein Sac7d sharply kinks DNA
    • Robinson, H. et al. The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature 392, 202-205 (1998).
    • (1998) Nature , vol.392 , pp. 202-205
    • Robinson, H.1
  • 26
    • 0033553405 scopus 로고    scopus 로고
    • Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA
    • Odell, M. & Shuman, S. Footprinting of Chlorella virus DNA ligase bound at a nick in duplex DNA. J. Biol. Chem. 274, 14032-14039 (1999).
    • (1999) J. Biol. Chem. , vol.274 , pp. 14032-14039
    • Odell, M.1    Shuman, S.2
  • 27
    • 0034635347 scopus 로고    scopus 로고
    • Nick recognition by DNA ligases
    • Doherty, A. J. & Dafforn, T. R. Nick recognition by DNA ligases. J. Mol. Biol. 296, 43-56 (2000).
    • (2000) J. Mol. Biol. , vol.296 , pp. 43-56
    • Doherty, A.J.1    Dafforn, T.R.2
  • 28
    • 0030767872 scopus 로고    scopus 로고
    • Ligation of RNA-containing duplexes by vaccinia DNA ligase
    • Sekiguchi, J. & Shuman, S. Ligation of RNA-containing duplexes by vaccinia DNA ligase. Biochemistry 36, 9073-9079 (1997).
    • (1997) Biochemistry , vol.36 , pp. 9073-9079
    • Sekiguchi, J.1    Shuman, S.2
  • 29
    • 0030929525 scopus 로고    scopus 로고
    • Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing
    • Rumbaugh, J. A., Murante, R. S., Shi, S. & Bambara, R. A. Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing. J. Biol. Chem. 272, 22591-22599 (1997).
    • (1997) J. Biol. Chem. , vol.272 , pp. 22591-22599
    • Rumbaugh, J.A.1    Murante, R.S.2    Shi, S.3    Bambara, R.A.4
  • 30
    • 0032145356 scopus 로고    scopus 로고
    • Specificity and fidelity of strand joining by Chlorella virus DNA ligase
    • Sriskanda, V. & Shuman, S. Specificity and fidelity of strand joining by Chlorella virus DNA ligase. Nucleic Acids Res. 26, 3536-3541 (1998).
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3536-3541
    • Sriskanda, V.1    Shuman, S.2
  • 31
    • 0028846525 scopus 로고
    • Vaccinia virus DNA ligase: Specificity, fidelity, and inhibition
    • Shuman, S. Vaccinia virus DNA ligase: specificity, fidelity, and inhibition. Biochemistry 34, 16138-16147 (1995).
    • (1995) Biochemistry , vol.34 , pp. 16138-16147
    • Shuman, S.1
  • 32
    • 0033569841 scopus 로고    scopus 로고
    • Delayed DNA joining at 3′ mismatches by human DNA ligases
    • Bhagwat, A. S., Sanderson, R. J. & Lindahl, T. Delayed DNA joining at 3′ mismatches by human DNA ligases. Nucleic Acids Res. 27, 4028-4033 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4028-4033
    • Bhagwat, A.S.1    Sanderson, R.J.2    Lindahl, T.3
  • 33
    • 4344569343 scopus 로고    scopus 로고
    • DNA ligases ensure fidelity by interrogating minor groove contacts
    • Liu, P., Burdzy, A. & Sowers, L. C. DNA ligases ensure fidelity by interrogating minor groove contacts. Nucleic Acids Res. 32, 4503-4511 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4503-4511
    • Liu, P.1    Burdzy, A.2    Sowers, L.C.3
  • 34
    • 2442599792 scopus 로고    scopus 로고
    • Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases
    • Corbett, K. D. & Berger, J. M. Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct. 33, 95-118 (2004).
    • (2004) Annu. Rev. Biophys. Biomol. Struct. , vol.33 , pp. 95-118
    • Corbett, K.D.1    Berger, J.M.2
  • 35
    • 0023801508 scopus 로고
    • AMP-dependent DNA relaxation catalyzed by DNA ligase occurs by a nicking-closing mechanism
    • Montecucco, A. & Ciarrocchi, G. AMP-dependent DNA relaxation catalyzed by DNA ligase occurs by a nicking-closing mechanism. Nucleic Acids Res. 16, 7369-7381 (1988).
    • (1988) Nucleic Acids Res. , vol.16 , pp. 7369-7381
    • Montecucco, A.1    Ciarrocchi, G.2
  • 36
    • 0033534370 scopus 로고    scopus 로고
    • Functional domains of an ATP-dependem DNA ligase
    • Doherty, A. J. & Wigley, D. B. Functional domains of an ATP-dependem DNA ligase. J. Mol. Biol. 285, 63-71 (1999).
    • (1999) J. Mol. Biol. , vol.285 , pp. 63-71
    • Doherty, A.J.1    Wigley, D.B.2
  • 37
    • 0032031972 scopus 로고    scopus 로고
    • PCNA binding through a conserved motif
    • Warbrick, E. PCNA binding through a conserved motif. Bioessays 20, 195-199 (1998).
    • (1998) Bioessays , vol.20 , pp. 195-199
    • Warbrick, E.1
  • 38
    • 0342350255 scopus 로고    scopus 로고
    • Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair
    • Levin, D. S., McKenna, A. E., Motycka, T. A., Matsumoto, Y. & Tomkinson, A. E. Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair. Curr. Biol. 10, 919-922 (2000).
    • (2000) Curr. Biol. , vol.10 , pp. 919-922
    • Levin, D.S.1    McKenna, A.E.2    Motycka, T.A.3    Matsumoto, Y.4    Tomkinson, A.E.5
  • 39
    • 0030692134 scopus 로고    scopus 로고
    • An interaction between DNA ligase I and proliferating cell nuclear antigen: Implications for Okazaki fragment synthesis and joining
    • Levin, D. S., Bai, W., Yao, N., O'Donnell, M. & Tomkinson, A. E. An interaction between DNA ligase I and proliferating cell nuclear antigen: implications for Okazaki fragment synthesis and joining. Proc. Natl Acad. Sci. USA 94, 12863-12868 (1997).
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 12863-12868
    • Levin, D.S.1    Bai, W.2    Yao, N.3    O'Donnell, M.4    Tomkinson, A.E.5
  • 40
    • 0037251411 scopus 로고    scopus 로고
    • A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus
    • Dionne, I., Nookala, R. K., Jackson, S. P., Doherty, A. I. & Bell, S. D. A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Cell 11, 275-282 (2003).
    • (2003) Mol. Cell , vol.11 , pp. 275-282
    • Dionne, I.1    Nookala, R.K.2    Jackson, S.P.3    Doherty, A.I.4    Bell, S.D.5
  • 41
    • 0027420787 scopus 로고
    • Expression of active human DNA ligase I in Escherichia coli cells that harbor a full-length DNA ligase I cDNA construct
    • Teraoka, H. et al. Expression of active human DNA ligase I in Escherichia coli cells that harbor a full-length DNA ligase I cDNA construct. J. Biol. Chem. 268, 24156-24162 (1993).
    • (1993) J. Biol. Chem. , vol.268 , pp. 24156-24162
    • Teraoka, H.1
  • 42
    • 0027439390 scopus 로고
    • Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin
    • Van Duyne, G. D., Standaert, R. E., Karplus, P. A., Schreiber, S. L. & Clardy, J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105-124 (1993).
    • (1993) J. Mol. Biol. , vol.229 , pp. 105-124
    • Van Duyne, G.D.1    Standaert, R.E.2    Karplus, P.A.3    Schreiber, S.L.4    Clardy, J.5
  • 43
    • 0031059866 scopus 로고    scopus 로고
    • (eds Carter, C. W. & Sweet, R. M.) (Academic, New York)
    • Otwinowski, Z. & Minor, W. in Methods Enzymology (eds Carter, C. W. & Sweet, R. M.) 307-326 (Academic, New York, 1997).
    • (1997) Methods Enzymology , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 45
    • 0031058188 scopus 로고    scopus 로고
    • (eds Sweet, R. M. & Carter, C. W.) (Academic, New York)
    • La Fortelle, E. D. & Bricogne, G. in Methods Enzymology (eds Sweet, R. M. & Carter, C. W.) 472-494 (Academic, New York, 1997).
    • (1997) Methods Enzymology , pp. 472-494
    • La Fortelle, E.D.1    Bricogne, G.2
  • 46
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
    • (1991) Acta Crystallogr. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard4
  • 47
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography & NMR system: A new software suite for macromolecular structure determination
    • Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921 (1998).
    • (1998) Acta Crystallogr. D Biol. Crystallogr. , vol.54 , pp. 905-921
    • Brunger, A.T.1
  • 48
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G. N. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255 (1997).
    • (1997) Acta Crystallogr. D Biol. Crystallogr. , vol.53 , pp. 240-255
    • Murshudov, G.N.1
  • 49
    • 0028850148 scopus 로고
    • The N-terminal domain of human DNA ligase I contains the nuclear localization signal and directs the enzyme to sites of DNA replication
    • Montecucco, A. et al. The N-terminal domain of human DNA ligase I contains the nuclear localization signal and directs the enzyme to sites of DNA replication. EMBO J. 14, 5379-5386 (1995).
    • (1995) EMBO J. , vol.14 , pp. 5379-5386
    • Montecucco, A.1
  • 50
    • 0032493630 scopus 로고    scopus 로고
    • Thermodynamics of human DNA ligase I trimerization and association with DNA polymerase β
    • Dimitriadis, E. K. et al. Thermodynamics of human DNA ligase I trimerization and association with DNA polymerase β. J. Biol. Chem. 273, 20540-20550 (1998).
    • (1998) J. Biol. Chem. , vol.273 , pp. 20540-20550
    • Dimitriadis, E.K.1


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