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Volumn 52, Issue 29, 2013, Pages 4881-4890

Following DNA chain extension and protein conformational changes in crystals of a y-family DNA polymerase via raman crystallography

Author keywords

[No Author keywords available]

Indexed keywords

BINARY AND TERNARY COMPLEXES; CATALYTIC METALS; CONFORMATIONAL CHANGE; PRIMER EXTENSION; PROTEIN CONFORMATIONAL CHANGES; RAMAN INTENSITIES; RAMAN MICROSCOPY; SULFOLOBUS SOLFATARICUS;

EID: 84880582585     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi400524h     Document Type: Article
Times cited : (9)

References (40)
  • 3
    • 0035209666 scopus 로고    scopus 로고
    • Detecting, signalling and repairing DNA double-strand breaks
    • Jackson, S. P. (2001) Detecting, signalling and repairing DNA double-strand breaks Biochem. Soc. Trans. 29, 655-661
    • (2001) Biochem. Soc. Trans. , vol.29 , pp. 655-661
    • Jackson, S.P.1
  • 5
    • 0027227875 scopus 로고
    • Nucleotide sequence of the gene for a 74 kDa DNA polymerase from the archaeon Sulfolobus solfataricus
    • Prangishvili, D. and Klenk, H. P. (1993) Nucleotide sequence of the gene for a 74 kDa DNA polymerase from the archaeon Sulfolobus solfataricus Nucleic Acids Res. 21, 2768
    • (1993) Nucleic Acids Res. , vol.21 , pp. 2768
    • Prangishvili, D.1    Klenk, H.P.2
  • 6
    • 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., and Yang, W. (2001) Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication Cell 107, 91-102
    • (2001) Cell , vol.107 , pp. 91-102
    • Ling, H.1    Boudsocq, F.2    Woodgate, R.3    Yang, W.4
  • 7
    • 43049105331 scopus 로고    scopus 로고
    • Snapshots of a Y-Family DNA Polymerase in Replication: Substrate-induced Conformational Transitions and Implications for Fidelity of Dpo4
    • Wong, J. H., Fiala, K. A., Suo, Z., and Ling, H. (2008) Snapshots of a Y-Family DNA Polymerase in Replication: Substrate-induced Conformational Transitions and Implications for Fidelity of Dpo4 J. Mol. Biol. 379, 317-330
    • (2008) J. Mol. Biol. , vol.379 , pp. 317-330
    • Wong, J.H.1    Fiala, K.A.2    Suo, Z.3    Ling, H.4
  • 9
    • 0034720285 scopus 로고    scopus 로고
    • Low fidelity DNA synthesis by human DNA polymerase η
    • Matsuda, T., Bebenek, K., Masutani, C., Hanaoka, F., and Kunkel, T. A. (2000) Low fidelity DNA synthesis by human DNA polymerase η Nature 404, 1011-1013
    • (2000) Nature , vol.404 , pp. 1011-1013
    • Matsuda, T.1    Bebenek, K.2    Masutani, C.3    Hanaoka, F.4    Kunkel, T.A.5
  • 10
    • 0034738983 scopus 로고    scopus 로고
    • Eukaryotic polymerases ι and ζ act sequentially to bypass DNA lesions
    • Johnson, R. E., Washington, M. T., Haracska, L., Prakash, S., and Prakash, L. (2000) Eukaryotic polymerases ι and ζ act sequentially to bypass DNA lesions Nature 406, 1015-1019
    • (2000) Nature , vol.406 , pp. 1015-1019
    • Johnson, R.E.1    Washington, M.T.2    Haracska, L.3    Prakash, S.4    Prakash, L.5
  • 13
    • 0034327552 scopus 로고    scopus 로고
    • Human DNA polymerase κ synthesizes DNA with extraordinarily low fidelity
    • Zhang, Y., Yuan, F., Xin, H., Wu, X., Rajpal, D. K., Yang, D., and Wang, Z. (2000) Human DNA polymerase κ synthesizes DNA with extraordinarily low fidelity Nucleic Acids Res. 28, 4147-4156
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4147-4156
    • Zhang, Y.1    Yuan, F.2    Xin, H.3    Wu, X.4    Rajpal, D.K.5    Yang, D.6    Wang, Z.7
  • 14
    • 0035850235 scopus 로고    scopus 로고
    • Translesion synthesis by the UmuC family of DNA polymerases
    • Wang, Z. (2001) Translesion synthesis by the UmuC family of DNA polymerases Mutat. Res., DNA Repair 486, 59-70
    • (2001) Mutat. Res., DNA Repair , vol.486 , pp. 59-70
    • Wang, Z.1
  • 15
    • 2542571187 scopus 로고    scopus 로고
    • Pre-Steady-State Kinetic Studies of the Fidelity and Mechanism of Polymerization Catalyzed by Truncated Human DNA Polymerase λ
    • Fiala, K. A., Abdel-Gawad, W., and Suo, Z. (2004) Pre-Steady-State Kinetic Studies of the Fidelity and Mechanism of Polymerization Catalyzed by Truncated Human DNA Polymerase λ Biochemistry 43, 6751-6762
    • (2004) Biochemistry , vol.43 , pp. 6751-6762
    • Fiala, K.A.1    Abdel-Gawad, W.2    Suo, Z.3
  • 16
    • 1242307762 scopus 로고    scopus 로고
    • Mechanism of DNA Polymerization Catalyzed by Sulfolobus solfataricus P2 DNA Polymerase IV
    • Fiala, K. A. and Suo, Z. (2004) Mechanism of DNA Polymerization Catalyzed by Sulfolobus solfataricus P2 DNA Polymerase IV Biochemistry 43, 2116-2125
    • (2004) Biochemistry , vol.43 , pp. 2116-2125
    • Fiala, K.A.1    Suo, Z.2
  • 17
    • 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
  • 18
    • 41849102779 scopus 로고    scopus 로고
    • Mechanistic consequences of temperature on DNA polymerization catalyzed by a Y-family DNA polymerase
    • Fiala, K. A., Sherrer, S. M., Brown, J. A., and Suo, Z. (2008) Mechanistic consequences of temperature on DNA polymerization catalyzed by a Y-family DNA polymerase Nucleic Acids Res. 36, 1990-2001
    • (2008) Nucleic Acids Res. , vol.36 , pp. 1990-2001
    • Fiala, K.A.1    Sherrer, S.M.2    Brown, J.A.3    Suo, Z.4
  • 19
    • 70350508554 scopus 로고    scopus 로고
    • Global conformational dynamics of a Y-family DNA polymerase during catalysis
    • Xu, C., Maxwell, B. A., Brown, J. A., Zhang, L., and Suo, Z. (2009) Global conformational dynamics of a Y-family DNA polymerase during catalysis PLoS Biol. 7, e1000225
    • (2009) PLoS Biol. , vol.7 , pp. 1000225
    • Xu, C.1    Maxwell, B.A.2    Brown, J.A.3    Zhang, L.4    Suo, Z.5
  • 20
    • 23044492225 scopus 로고    scopus 로고
    • Motions of the fingers subdomain of Klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases
    • Rothwell, P. J., Mitaksov, V., and Waksman, G. (2005) Motions of the fingers subdomain of Klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases Mol. Cell 19, 345-355
    • (2005) Mol. Cell , vol.19 , pp. 345-355
    • Rothwell, P.J.1    Mitaksov, V.2    Waksman, G.3
  • 21
    • 39549088486 scopus 로고    scopus 로고
    • An intramolecular FRET system monitors fingers subdomain opening in Klentaq1
    • Allen, W. J., Rothwell, P. J., and Waksman, G. (2008) An intramolecular FRET system monitors fingers subdomain opening in Klentaq1 Protein Sci. 17, 401-408
    • (2008) Protein Sci. , vol.17 , pp. 401-408
    • Allen, W.J.1    Rothwell, P.J.2    Waksman, G.3
  • 22
    • 44949114390 scopus 로고    scopus 로고
    • Fingers-Closing and Other Rapid Conformational Changes in DNA Polymerase i (Klenow Fragment) and Their Role in Nucleotide Selectivity
    • Joyce, C. M., Potapova, O., DeLucia, A. M., Huang, X., Basu, V. P., and Grindley, N. D. F. (2008) Fingers-Closing and Other Rapid Conformational Changes in DNA Polymerase I (Klenow Fragment) and Their Role in Nucleotide Selectivity Biochemistry 47, 6103-6116
    • (2008) Biochemistry , vol.47 , pp. 6103-6116
    • Joyce, C.M.1    Potapova, O.2    Delucia, A.M.3    Huang, X.4    Basu, V.P.5    Grindley, N.D.F.6
  • 23
    • 84863676249 scopus 로고    scopus 로고
    • Watching DNA polymerase η make a phosphodiester bond
    • Nakamura, T., Zhao, Y., Yamagata, Y., Hua, Y.-j., and Yang, W. (2012) Watching DNA polymerase η make a phosphodiester bond Nature 487, 196-201
    • (2012) Nature , vol.487 , pp. 196-201
    • Nakamura, T.1    Zhao, Y.2    Yamagata, Y.3    Hua, Y.-J.4    Yang, W.5
  • 24
    • 0032518524 scopus 로고    scopus 로고
    • Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
    • Kiefer, J. R., Mao, C., Braman, J. C., and Beese, L. S. (1998) Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal Nature 391, 304-307
    • (1998) Nature , vol.391 , pp. 304-307
    • Kiefer, J.R.1    Mao, C.2    Braman, J.C.3    Beese, L.S.4
  • 25
    • 33646727439 scopus 로고    scopus 로고
    • Raman crystallography and other biochemical applications of Raman microscopy
    • Carey, P. R. (2006) Raman crystallography and other biochemical applications of Raman microscopy Annu. Rev. Phys. Chem. 57, 527-554
    • (2006) Annu. Rev. Phys. Chem. , vol.57 , pp. 527-554
    • Carey, P.R.1
  • 28
    • 1542276786 scopus 로고    scopus 로고
    • Raman Spectroscopic Characterization of Secondary Structure in Natively Unfolded Proteins: α-Synuclein
    • Maiti, N. C., Apetri, M. M., Zagorski, M. G., Carey, P. R., and Anderson, V. E. (2004) Raman Spectroscopic Characterization of Secondary Structure in Natively Unfolded Proteins: α-Synuclein J. Am. Chem. Soc. 126, 2399-2408
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 2399-2408
    • Maiti, N.C.1    Apetri, M.M.2    Zagorski, M.G.3    Carey, P.R.4    Anderson, V.E.5
  • 29
    • 0033616633 scopus 로고    scopus 로고
    • Raman Markers of Nonaromatic Side Chains in an α-Helix Assembly: Ala, Asp, Glu, Gly, Ile, Leu, Lys, Ser, and Val Residues of Phage fd Subunits
    • Overman, S. A. and Thomas, G. J., Jr. (1999) Raman Markers of Nonaromatic Side Chains in an α-Helix Assembly: Ala, Asp, Glu, Gly, Ile, Leu, Lys, Ser, and Val Residues of Phage fd Subunits Biochemistry 38, 4018-4027
    • (1999) Biochemistry , vol.38 , pp. 4018-4027
    • Overman, S.A.1    Thomas, Jr.G.J.2
  • 30
    • 0028986185 scopus 로고
    • Polarized Raman spectra of oriented fibers of A DNA and B DNA: Anisotropic and isotropic local Raman tensors of base and backbone vibrations
    • Thomas, G. J., Jr., Benevides, J. M., Overman, S. A., Ueda, T., Ushizawa, K., Saitoh, M., and Tsuboi, M. (1995) Polarized Raman spectra of oriented fibers of A DNA and B DNA: Anisotropic and isotropic local Raman tensors of base and backbone vibrations Biophys. J. 68, 1073-1088
    • (1995) Biophys. J. , vol.68 , pp. 1073-1088
    • Thomas, Jr.G.J.1    Benevides, J.M.2    Overman, S.A.3    Ueda, T.4    Ushizawa, K.5    Saitoh, M.6    Tsuboi, M.7
  • 31
    • 0034646323 scopus 로고    scopus 로고
    • -1 as an Indicator of Protein α-Helix Orientation: Application to Pf1 Filamentous Virus
    • -1 as an Indicator of Protein α-Helix Orientation: Application to Pf1 Filamentous Virus Biochemistry 39, 2677-2684
    • (2000) Biochemistry , vol.39 , pp. 2677-2684
    • Tsuboi, M.1    Suzuki, M.2    Overman, S.A.3    Thomas, Jr.G.J.4
  • 32
    • 80051601456 scopus 로고    scopus 로고
    • Time-Resolved Events on the Reaction Pathway of Transcript Initiation by a Single-Subunit RNA Polymerase: Raman Crystallographic Evidence
    • Chen, Y., Basu, R., Gleghorn, M. L., Murakami, K. S., and Carey, P. R. (2011) Time-Resolved Events on the Reaction Pathway of Transcript Initiation by a Single-Subunit RNA Polymerase: Raman Crystallographic Evidence J. Am. Chem. Soc. 133, 12544-12555
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 12544-12555
    • Chen, Y.1    Basu, R.2    Gleghorn, M.L.3    Murakami, K.S.4    Carey, P.R.5
  • 34
    • 27144542782 scopus 로고    scopus 로고
    • Fidelity of Dpo4: Effect of metal ions, nucleotide selection and pyrophosphorolysis
    • Vaisman, A., Ling, H., Woodgate, R., and Yang, W. (2005) Fidelity of Dpo4: Effect of metal ions, nucleotide selection and pyrophosphorolysis EMBO J. 24, 2957-2967
    • (2005) EMBO J. , vol.24 , pp. 2957-2967
    • Vaisman, A.1    Ling, H.2    Woodgate, R.3    Yang, W.4
  • 35
    • 0345254956 scopus 로고    scopus 로고
    • Following the Reactions of Mechanism-Based Inhibitors with β-Lactamase by Raman Crystallography
    • Helfand, M. S., Totir, M. A., Carey, M. P., Hujer, A. M., Bonomo, R. A., and Carey, P. R. (2003) Following the Reactions of Mechanism-Based Inhibitors with β-Lactamase by Raman Crystallography Biochemistry 42, 13386-13392
    • (2003) Biochemistry , vol.42 , pp. 13386-13392
    • Helfand, M.S.1    Totir, M.A.2    Carey, M.P.3    Hujer, A.M.4    Bonomo, R.A.5    Carey, P.R.6
  • 36
    • 0942290637 scopus 로고    scopus 로고
    • Tazobactam Forms a Stoichiometric trans-Enamine Intermediate in the E166A Variant of SHV-1 β-Lactamase: 1.63 Å Crystal Structure
    • Padayatti, P. S., Helfand, M. S., Totir, M. A., Carey, M. P., Hujer, A. M., Carey, P. R., Bonomo, R. A., and van den Akker, F. (2004) Tazobactam Forms a Stoichiometric trans-Enamine Intermediate in the E166A Variant of SHV-1 β-Lactamase: 1.63 Å Crystal Structure Biochemistry 43, 843-848
    • (2004) Biochemistry , vol.43 , pp. 843-848
    • Padayatti, P.S.1    Helfand, M.S.2    Totir, M.A.3    Carey, M.P.4    Hujer, A.M.5    Carey, P.R.6    Bonomo, R.A.7    Van Den Akker, F.8
  • 37
    • 84873284245 scopus 로고    scopus 로고
    • Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography
    • Basu, R. S. and Murakami, K. S. (2013) Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography J. Biol. Chem. 288, 3305-3311
    • (2013) J. Biol. Chem. , vol.288 , pp. 3305-3311
    • Basu, R.S.1    Murakami, K.S.2
  • 39
    • 80051601456 scopus 로고    scopus 로고
    • Time-Resoled Evens on the Reaction Pathway of Transcrip Initiation by a Single-Subunit RNA Polymerase: Raman Crystallographic Evidence
    • Chen, Y., Basu, R., Gleorn, M. L., Muakami, K. S., and Caey, P. R. (2011) Time-Resoled Evens on the Reaction Pathway of Transcrip Initiation by a Single-Subunit RNA Polymerase: Raman Crystallographic Evidence J. Am. Chem. Soc. 133, 12544-12555
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 12544-12555
    • Chen, Y.1    Basu, R.2    Gleorn, M.L.3    Muakami, K.S.4    Caey, P.R.5
  • 40
    • 84873284245 scopus 로고    scopus 로고
    • Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography
    • Basu, R. S. and Murakami, K. S. (2013) Watching the Bacteriophage N4 RNA Polymerase Transcription by Time-dependent Soak-trigger-freeze X-ray Crystallography J. Biol. Chem. 288, 3305-3311
    • (2013) J. Biol. Chem. , vol.288 , pp. 3305-3311
    • Basu, R.S.1    Murakami, K.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.