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Volumn 39, Issue 4, 2011, Pages 1554-1564

Hpy188I-DNA pre- and post-cleavage complexes - Snapshots of the GIY-YIG nuclease mediated catalysis

Author keywords

[No Author keywords available]

Indexed keywords

GIY YIG NUCLEASE; METAL ION; NUCLEASE; UNCLASSIFIED DRUG;

EID: 79952332536     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq821     Document Type: Article
Times cited : (26)

References (52)
  • 1
    • 33748867012 scopus 로고    scopus 로고
    • Phylogenomic analysis of the GIY-YIG nuclease superfamily
    • Dunin-Horkawicz, S., Feder, M. and Bujnicki, J.M. (2006) Phylogenomic analysis of the GIY-YIG nuclease superfamily. BMC Genomics, 7, 98.
    • (2006) BMC Genomics , vol.7 , pp. 98
    • Dunin-Horkawicz, S.1    Feder, M.2    Bujnicki, J.M.3
  • 2
    • 0036828959 scopus 로고    scopus 로고
    • Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease i-TevI
    • Van Roey, P., Meehan, L., Kowalski, J.C., Belfort, M. and Derbyshire, V. (2002) Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Nat. Struct. Biol., 9, 806-811. (Pubitemid 35257778)
    • (2002) Nature Structural Biology , vol.9 , Issue.11 , pp. 806-811
    • Van Roey, P.1    Meehan, L.2    Kowalski, J.C.3    Belfort, M.4    Derbyshire, V.5
  • 4
    • 49449103183 scopus 로고    scopus 로고
    • Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis
    • Lagerback, P. and Carlson, K. (2008) Amino acid residues in the GIY-YIG endonuclease II of phage T4 affecting sequence recognition and binding as well as catalysis. J. Bacteriol., 190, 5533-5544.
    • (2008) J. Bacteriol. , vol.190 , pp. 5533-5544
    • Lagerback, P.1    Carlson, K.2
  • 5
    • 77950019411 scopus 로고    scopus 로고
    • Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme
    • Andersson, C.E., Lagerback, P. and Carlson, K. (2010) Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme. J. Mol. Biol., 397, 1003-1016.
    • (2010) J. Mol. Biol. , vol.397 , pp. 1003-1016
    • Andersson, C.E.1    Lagerback, P.2    Carlson, K.3
  • 6
    • 0033562780 scopus 로고    scopus 로고
    • Configuration of the catalytic GIY-YIG domain of intron endonuclease I-Tevl: Coincidence of computational and molecular findings
    • DOI 10.1093/nar/27.10.2115
    • Kowalski, J.C., Belfort, M., Stapleton, M.A., Holpert, M., Dansereau, J.T., Pietrokovski, S., Baxter, S.M. and Derbyshire, V. (1999) Configuration of the catalytic GIY-YIG domain of intronendonuclease I-TevI: coincidence of computational and molecular findings. Nucleic Acids Res., 27, 2115-2125. (Pubitemid 29219240)
    • (1999) Nucleic Acids Research , vol.27 , Issue.10 , pp. 2115-2125
    • Kowalski, J.C.1    Belfort, M.2    Stapleton, M.A.3    Holpert, M.4    Dansereau, J.T.5    Pietrokovski, S.6    Baxter, S.M.7    Derbyshire, V.8
  • 7
    • 0031556945 scopus 로고    scopus 로고
    • Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site
    • DOI 10.1006/jmbi.1996.0754
    • Derbyshire, V., Kowalski, J.C., Dansereau, J.T., Hauer, C.R. and Belfort, M. (1997) Two-domain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site. J. Mol. Biol., 265, 494-506. (Pubitemid 27113036)
    • (1997) Journal of Molecular Biology , vol.265 , Issue.5 , pp. 494-506
    • Derbyshire, V.1    Kowalski, J.C.2    Dansereau, J.T.3    Hauer, C.R.4    Belfort, M.5
  • 8
    • 0034595822 scopus 로고    scopus 로고
    • Purification of the novel endonuclease, Hpy188I, and cloning of its restriction-modification genes reveal evidence of its horizontal transfer to the Helicobacter pylori genome
    • DOI 10.1074/jbc.M910303199
    • Xu, Q., Stickel, S., Roberts, R.J., Blaser, M.J. and Morgan, R.D. (2000) Purification of the novel endonuclease, Hpy188I, and cloning of its restriction-modification genes reveal evidence of its horizontal transfer to the Helicobacter pylori genome. J. Biol. Chem., 275, 17086-17093. (Pubitemid 30398952)
    • (2000) Journal of Biological Chemistry , vol.275 , Issue.22 , pp. 17086-17093
    • Xu, Q.1    Stickel, S.2    Roberts, R.J.3    Blaser, M.J.4    Morgan, R.D.5
  • 9
    • 33644619706 scopus 로고    scopus 로고
    • Prokaryotic nucleotide excision repair: The UvrABC system
    • Truglio, J.J., Croteau, D.L., Van Houten, B. and Kisker, C. (2006) Prokaryotic nucleotide excision repair: the UvrABC system. Chem. Rev., 106, 233-252.
    • (2006) Chem. Rev. , vol.106 , pp. 233-252
    • Truglio, J.J.1    Croteau, D.L.2    Van Houten, B.3    Kisker, C.4
  • 10
    • 39149131021 scopus 로고    scopus 로고
    • Cooperative damage recognition by UvrA and UvrB: Identification of UvrA residues that mediate DNA binding
    • Croteau, D.L., DellaVecchia, M.J., Perera, L. and Van Houten, B. (2008) Cooperative damage recognition by UvrA and UvrB: identification of UvrA residues that mediate DNA binding. DNA Repair, 7, 392-404.
    • (2008) DNA Repair , vol.7 , pp. 392-404
    • Croteau, D.L.1    Dellavecchia, M.J.2    Perera, L.3    Van Houten, B.4
  • 11
    • 33846531362 scopus 로고    scopus 로고
    • Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad
    • DOI 10.1038/sj.emboj.7601497, PII 7601497
    • Karakas, E., Truglio, J.J., Croteau, D., Rhau, B., Wang, L., Van Houten, B. and Kisker, C. (2007) Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad. EMBO J., 26, 613-622. (Pubitemid 46160960)
    • (2007) EMBO Journal , vol.26 , Issue.2 , pp. 613-622
    • Karakas, E.1    Truglio, J.J.2    Croteau, D.3    Rhau, B.4    Wang, L.5    Van Houten, B.6    Kisker, C.7
  • 14
    • 0347990576 scopus 로고    scopus 로고
    • Slx1-Slx4 Are Subunits of a Structure-specific Endonuclease That Maintains Ribosomal DNA in Fission Yeast
    • DOI 10.1091/mbc.E03-08-0586
    • Coulon, S., Gaillard, P.H., Chahwan, C., McDonald, W.H., Yates, J.R. III and Russell, P. (2004) Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol. Biol. Cell, 15, 71-80. (Pubitemid 38044944)
    • (2004) Molecular Biology of the Cell , vol.15 , Issue.1 , pp. 71-80
    • Coulon, S.1    Gaillard, P.-H.L.2    Chahwan, C.3    McDonald, W.H.4    Yates III, J.R.5    Russell, P.6
  • 15
    • 0038167328 scopus 로고    scopus 로고
    • Slx1 - Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1 - Top3
    • DOI 10.1101/gad.1105203
    • Fricke, W.M. and Brill, S.J. (2003) Slx1-Slx4 is a second structure-specific endonuclease functionally redundant with Sgs1-Top3. Genes Dev., 17, 1768-1778. (Pubitemid 36870339)
    • (2003) Genes and Development , vol.17 , Issue.14 , pp. 1768-1778
    • Fricke, W.M.1    Brill, S.J.2
  • 16
    • 67649636091 scopus 로고    scopus 로고
    • Control of genome stability by SLX protein complexes
    • Rouse, J. (2009) Control of genome stability by SLX protein complexes. Biochem. Soc. Trans., 37, 495-510.
    • (2009) Biochem. Soc. Trans. , vol.37 , pp. 495-510
    • Rouse, J.1
  • 20
    • 0343067128 scopus 로고    scopus 로고
    • Intronic GIY-YIG endonuclease gene in the mitochondrial genome of Podospora curvicolla: Evidence for mobility
    • Saguez, C., Lecellier, G. and Koll, F. (2000) Intronic GIY-YIG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility. Nucleic Acids Res., 28, 1299-1306. (Pubitemid 30142671)
    • (2000) Nucleic Acids Research , vol.28 , Issue.6 , pp. 1299-1306
    • Saguez, C.1    Lecellier, G.2    Koll, F.3
  • 22
    • 33644756595 scopus 로고    scopus 로고
    • Homing endonuclease structure and function
    • DOI 10.1017/S0033583505004063, PII S0033583505004063
    • Stoddard, B.L. (2005) Homing endonuclease structure and function. Q. Rev. Biophys., 38, 49-95. (Pubitemid 43338672)
    • (2005) Quarterly Reviews of Biophysics , vol.38 , Issue.1 , pp. 49-95
    • Stoddard, B.L.1
  • 23
    • 0035898540 scopus 로고    scopus 로고
    • Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate
    • DOI 10.1093/emboj/20.14.3631
    • Van Roey, P., Waddling, C.A., Fox, K.M., Belfort, M. and Derbyshire, V. (2001) Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate. EMBO J., 20, 3631-3637. (Pubitemid 32691774)
    • (2001) EMBO Journal , vol.20 , Issue.14 , pp. 3631-3637
    • Van Roey, P.1    Waddling, C.A.2    Fox, K.M.3    Belfort, M.4    Derbyshire, V.5
  • 24
    • 60849102182 scopus 로고    scopus 로고
    • Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily but exhibits an unusual active site
    • Kaminska, K.H., Kawai, M., Boniecki, M., Kobayashi, I. and Bujnicki, J.M. (2008) Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. BMC Struct. Biol., 8, 48.
    • (2008) BMC Struct. Biol. , vol.8 , pp. 48
    • Kaminska, K.H.1    Kawai, M.2    Boniecki, M.3    Kobayashi, I.4    Bujnicki, J.M.5
  • 26
    • 46349101158 scopus 로고    scopus 로고
    • Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
    • DOI 10.1093/nar/gkn175
    • Orlowski, J. and Bujnicki, J.M. (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res., 36, 3552-3569. (Pubitemid 351917520)
    • (2008) Nucleic Acids Research , vol.36 , Issue.11 , pp. 3552-3569
    • Orlowski, J.1    Bujnicki, J.M.2
  • 27
    • 0035883723 scopus 로고    scopus 로고
    • Structure and function of type II restriction endonucleases
    • Pingoud, A. and Jeltsch, A. (2001) Structure and function of type II restriction endonucleases. Nucleic Acids Res., 29, 3705-3727. (Pubitemid 32910514)
    • (2001) Nucleic Acids Research , vol.29 , Issue.18 , pp. 3705-3727
    • Pingoud, A.1    Jeltsch, A.2
  • 28
    • 67649888360 scopus 로고    scopus 로고
    • Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA
    • Sokolowska, M., Czapinska, H. and Bochtler, M. (2009) Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA. Nucleic Acids Res, 37, 3799-3810.
    • (2009) Nucleic Acids Res , vol.37 , pp. 3799-3810
    • Sokolowska, M.1    Czapinska, H.2    Bochtler, M.3
  • 34
    • 0019376425 scopus 로고
    • DNA topoisomerases
    • Gellert, M. (1981) DNA topoisomerases. Annu. Rev. Biochem., 50, 879-910.
    • (1981) Annu. Rev. Biochem. , vol.50 , pp. 879-910
    • Gellert, M.1
  • 35
    • 0030886293 scopus 로고    scopus 로고
    • Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse
    • DOI 10.1038/37925
    • Guo, F., Gopaul, D.N. and van Duyne, G.D. (1997) Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature, 389, 40-46. (Pubitemid 27387683)
    • (1997) Nature , vol.389 , Issue.6646 , pp. 40-46
    • Guo, F.1    Gopaul, D.N.2    Van Duyne, G.D.3
  • 37
    • 0027439390 scopus 로고
    • Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin
    • DOI 10.1006/jmbi.1993.1012
    • Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L. and Clardy, J. (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol., 229, 105-124. (Pubitemid 23037917)
    • (1993) Journal of Molecular Biology , vol.229 , Issue.1 , pp. 105-124
    • Van Duyne, G.D.1    Standaert, R.F.2    Karplus, P.A.3    Schreiber, S.L.4    Clardy, J.5
  • 40
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project Number 4.
    • Collaborative Computational Project Number 4. (1994) The CCP4 suite: programs for protein crystallography. Acta. Crystallogr. D Biol. Crystallogr., 50, 760-763.
    • (1994) Acta. Crystallogr. D Biol. Crystallogr. , vol.50 , pp. 760-763
  • 41
    • 0002583957 scopus 로고
    • DM: An automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newslett
    • Cowtan, K. (1994) DM: an automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newslett. Protein Crystallogr., 31, 34-38.
    • (1994) Protein Crystallogr. , vol.31 , pp. 34-38
    • Cowtan, K.1
  • 42
    • 0347383760 scopus 로고    scopus 로고
    • ARP/wARP and Automatic Interpretation of Protein Electron Density Maps
    • DOI 10.1016/S0076-6879(03)74011-7
    • Morris, R.J., Perrakis, A. and Lamzin, V.S. (2003) ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol., 374, 229-244. (Pubitemid 37531812)
    • (2003) Methods in Enzymology , vol.374 , pp. 229-244
    • Morris, R.J.1    Perrakis, A.2    Lamzin, V.S.3
  • 43
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • DOI 10.1093/nar/gkg680
    • Lu, X.J. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121. (Pubitemid 37441878)
    • (2003) Nucleic Acids Research , vol.31 , Issue.17 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 45
    • 0032790081 scopus 로고    scopus 로고
    • XtalView/Xfit - A versatile program for manipulating atomic coordinates and electron density
    • DOI 10.1006/jsbi.1999.4094
    • McRee, D.E. (1999) XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol., 125, 156-165. (Pubitemid 29402600)
    • (1999) Journal of Structural Biology , vol.125 , Issue.2-3 , pp. 156-165
    • McRee, D.E.1
  • 47
    • 34047245428 scopus 로고    scopus 로고
    • A Sliding Restriction Enzyme Pauses
    • DOI 10.1016/j.str.2007.04.001, PII S0969212607001141
    • Pingoud, A. and Wende, W. (2007) A sliding restriction enzyme pauses. Structure, 15, 391-393. (Pubitemid 46551732)
    • (2007) Structure , vol.15 , Issue.4 , pp. 391-393
    • Pingoud, A.1    Wende, W.2
  • 48
    • 0036143789 scopus 로고    scopus 로고
    • Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation
    • DOI 10.1038/nsb741
    • Horton, N.C., Dorner, L.F. and Perona, J.J. (2002) Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation. Nat. Struct. Biol., 9, 42-47. (Pubitemid 34049178)
    • (2002) Nature Structural Biology , vol.9 , Issue.1 , pp. 42-47
    • Horton, N.C.1    Dorner, L.F.2    Perona, J.J.3
  • 49
    • 0030046809 scopus 로고    scopus 로고
    • Intercalation, DNA kinking, and the control of transcription
    • Werner, M.H., Gronenborn, A.M. and Clore, G.M. (1996) Intercalation, DNA kinking, and the control of transcription. Science, 271, 778-784. (Pubitemid 26058927)
    • (1996) Science , vol.271 , Issue.5250 , pp. 778-784
    • Werner, M.H.1    Gronenborn, A.M.2    Clore, G.M.3
  • 50
    • 0033528762 scopus 로고    scopus 로고
    • A new method for determining the stereochemistry of DNA cleavage reactions: Application to the SfiI and HpaII restriction endonucleases and to the MuA transposase
    • Mizuuchi, K., Nobbs, T.J., Halford, S.E., Adzuma, K. and Qin, J. (1999) A new method for determining the stereochemistry of DNA cleavage reactions: application to the SfiI and HpaII restriction endonucleases and to the MuA transposase. Biochemistry, 38, 4640-4648.
    • (1999) Biochemistry , vol.38 , pp. 4640-4648
    • Mizuuchi, K.1    Nobbs, T.J.2    Halford, S.E.3    Adzuma, K.4    Qin, J.5


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