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Volumn 338, Issue 4, 2004, Pages 725-733

Crystal structure of BstYI at 1.85 Å resolution: A thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII

Author keywords

BamHI; BglII; BstYI; MAD, multiwavelength anomalous dispersion; Restriction endonuclease; Thermophilic

Indexed keywords

ADENINE; CORE PROTEIN; CYTOSINE; DIMER; DNA; DNA BASE; ENDONUCLEASE; GUANINE; NUCLEOTIDE; PROTEIN BAMHI; PROTEIN BG1II; PROTEIN BSTYI; RESTRICTION ENDONUCLEASE; THYMINE; UNCLASSIFIED DRUG;

EID: 1942425560     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.02.074     Document Type: Article
Times cited : (14)

References (36)
  • 2
    • 0002598414 scopus 로고
    • Type II restriction endonucleases
    • S.M. Linn, R.S. Lloyd, & R.J. Roberts. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
    • Roberts R.J., Halford S.E. Type II restriction endonucleases. Linn S.M., Lloyd R.S., Roberts R.J. Nucleases. 1993;35-88 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1993) Nucleases , pp. 35-88
    • Roberts, R.J.1    Halford, S.E.2
  • 3
    • 0141954129 scopus 로고    scopus 로고
    • Crystallographic and bioinformatic studies on restriction endonucleases: Inference of evolutionary relationships in the "midnight zone" of homology
    • Bujnicki J.M. Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. Curr. Protein Pept. Sci. 4:2003;327-337.
    • (2003) Curr. Protein Pept. Sci. , vol.4 , pp. 327-337
    • Bujnicki, J.M.1
  • 4
    • 0037082418 scopus 로고    scopus 로고
    • Crystal structure of the Bse634I restriction endonuclease: Comparison of two enzymes recognizing the same DNA sequence
    • Grazulis S., Deibert M., Rimseliene R., Skirgaila R., Sasnauskas G., Lagunavicius A., et al. Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucl. Acids Res. 30:2002;876-885.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 876-885
    • Grazulis, S.1    Deibert, M.2    Rimseliene, R.3    Skirgaila, R.4    Sasnauskas, G.5    Lagunavicius, A.6
  • 5
    • 0035883723 scopus 로고    scopus 로고
    • Structure and function of type II restriction endonucleases
    • Pingoud A., Jeltsch A. Structure and function of type II restriction endonucleases. Nucl. Acids Res. 29:2001;3705-3727.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 3705-3727
    • Pingoud, A.1    Jeltsch, A.2
  • 6
    • 0036143789 scopus 로고    scopus 로고
    • Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation
    • Horton N.C., Dorner L.F., Perona J.J. Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation. Nature Struct. Biol. 9:2002;42-47.
    • (2002) Nature Struct. Biol. , vol.9 , pp. 42-47
    • Horton, N.C.1    Dorner, L.F.2    Perona, J.J.3
  • 7
    • 0035096078 scopus 로고    scopus 로고
    • Restriction enzyme BsoBI-DNA complex: A tunnel for recognition of degenerate DNA sequences and potential histidine catalysis
    • van der Woerd M.J., Pelletier J.J., Xu S., Friedman A.M. Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Structure (Camb.). 9:2001;133-144.
    • (2001) Structure (Camb.) , vol.9 , pp. 133-144
    • Van Der Woerd, M.J.1    Pelletier, J.J.2    Xu, S.3    Friedman, A.M.4
  • 8
    • 0028932881 scopus 로고
    • Structure and function of restriction endonucleases
    • Aggarwal A.K. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5:1995;11-19.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 11-19
    • Aggarwal, A.K.1
  • 9
    • 0033933471 scopus 로고    scopus 로고
    • Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures
    • Bujnicki J.M. Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J. Mol. Evol. 50:2000;39-44.
    • (2000) J. Mol. Evol. , vol.50 , pp. 39-44
    • Bujnicki, J.M.1
  • 10
    • 0034660061 scopus 로고    scopus 로고
    • Crystal structure of NaeI - An evolutionary bridge between DNA endonuclease and topoisomerase
    • Huai Q., Colandene J.D., Chen Y., Luo F., Zhao Y., Topal M.D., Ke H. Crystal structure of NaeI - an evolutionary bridge between DNA endonuclease and topoisomerase. EMBO J. 19:2000;3110-3118.
    • (2000) EMBO J. , vol.19 , pp. 3110-3118
    • Huai, Q.1    Colandene, J.D.2    Chen, Y.3    Luo, F.4    Zhao, Y.5    Topal, M.D.6    Ke, H.7
  • 12
    • 0032555574 scopus 로고    scopus 로고
    • Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts
    • Horton N.C., Perona J.J. Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts. J. Biol. Chem. 273:1998;21721-21729.
    • (1998) J. Biol. Chem. , vol.273 , pp. 21721-21729
    • Horton, N.C.1    Perona, J.J.2
  • 13
    • 0034026486 scopus 로고    scopus 로고
    • On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: A case study employing EcoRV as the target
    • Lanio T., Jeltsch A., Pingoud A. On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target. Protein Eng. 13:2000;275-281.
    • (2000) Protein Eng. , vol.13 , pp. 275-281
    • Lanio, T.1    Jeltsch, A.2    Pingoud, A.3
  • 14
    • 0032533367 scopus 로고    scopus 로고
    • Protein engineering of the restriction endonuclease EcoRV - Structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site
    • Schottler S., Wenz C., Lanio T., Jeltsch A., Pingoud A. Protein engineering of the restriction endonuclease EcoRV - structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site. Eur. J. Biochem. 258:1998;184-191.
    • (1998) Eur. J. Biochem. , vol.258 , pp. 184-191
    • Schottler, S.1    Wenz, C.2    Lanio, T.3    Jeltsch, A.4    Pingoud, A.5
  • 15
    • 0033613907 scopus 로고    scopus 로고
    • Genetic analysis of the base-specific contacts of BamHI restriction endonuclease
    • Dorner L.F., Bitinaite J., Whitaker R.D., Schildkraut I. Genetic analysis of the base-specific contacts of BamHI restriction endonuclease. J. Mol. Biol. 285:1999;1515-1523.
    • (1999) J. Mol. Biol. , vol.285 , pp. 1515-1523
    • Dorner, L.F.1    Bitinaite, J.2    Whitaker, R.D.3    Schildkraut, I.4
  • 17
    • 0024589458 scopus 로고
    • Changing the hydrogen-bonding potential in the DNA binding site of EcoRI by site-directed mutagenesis drastically reduces the enzymatic activity, not, however, the preference of this restriction endonuclease for cleavage within the site-GAATTC
    • Alves J., Ruter T., Geiger R., Fliess A., Maass G., Pingoud A. Changing the hydrogen-bonding potential in the DNA binding site of EcoRI by site-directed mutagenesis drastically reduces the enzymatic activity, not, however, the preference of this restriction endonuclease for cleavage within the site-GAATTC. Biochemistry. 28:1989;2678-2684.
    • (1989) Biochemistry , vol.28 , pp. 2678-2684
    • Alves, J.1    Ruter, T.2    Geiger, R.3    Fliess, A.4    Maass, G.5    Pingoud, A.6
  • 18
    • 0032562147 scopus 로고    scopus 로고
    • Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site
    • Wenz C., Hahn M., Pingoud A. Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site. Biochemistry. 37:1998;2234-2242.
    • (1998) Biochemistry , vol.37 , pp. 2234-2242
    • Wenz, C.1    Hahn, M.2    Pingoud, A.3
  • 19
    • 0028989426 scopus 로고
    • Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants
    • Flores H., Osuna J., Heitman J., Soberon X. Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants. Gene. 157:1995;295-301.
    • (1995) Gene , vol.157 , pp. 295-301
    • Flores, H.1    Osuna, J.2    Heitman, J.3    Soberon, X.4
  • 20
    • 0029048413 scopus 로고
    • Structure of BamHI endonuclease bound to DNA: Partial folding and unfolding on DNA binding
    • Newman M., Strzelecka T., Dorner L.F., Schildkraut I., Aggarwal A.K. Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science. 269:1995;656-663.
    • (1995) Science , vol.269 , pp. 656-663
    • Newman, M.1    Strzelecka, T.2    Dorner, L.F.3    Schildkraut, I.4    Aggarwal, A.K.5
  • 21
    • 0028298842 scopus 로고
    • Structure of restriction endonuclease BamHI and its relationship to EcoRI
    • Newman M., Strzelecka T., Dorner L.F., Schildkraut I., Aggarwal A.K. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature. 368:1994;660-664.
    • (1994) Nature , vol.368 , pp. 660-664
    • Newman, M.1    Strzelecka, T.2    Dorner, L.F.3    Schildkraut, I.4    Aggarwal, A.K.5
  • 22
    • 0028773473 scopus 로고
    • Structure of restriction endonuclease BamHI phased at 1.95 Å resolution by MAD analysis
    • Newman M., Strzelecka T., Dorner L.F., Schildkraut I., Aggarwal A.K. Structure of restriction endonuclease BamHI phased at 1.95 Å resolution by MAD analysis. Structure. 2:1994;439-452.
    • (1994) Structure , vol.2 , pp. 439-452
    • Newman, M.1    Strzelecka, T.2    Dorner, L.F.3    Schildkraut, I.4    Aggarwal, A.K.5
  • 23
    • 0035147490 scopus 로고    scopus 로고
    • Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease
    • Lukacs C.M., Kucera R., Schildkraut I., Aggarwal A.K. Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease. Nature Struct. Biol. 8:2001;126-130.
    • (2001) Nature Struct. Biol. , vol.8 , pp. 126-130
    • Lukacs, C.M.1    Kucera, R.2    Schildkraut, I.3    Aggarwal, A.K.4
  • 24
    • 0033981010 scopus 로고    scopus 로고
    • Understanding the immutability of restriction enzymes: Crystal structure of BglII and its DNA substrate at 1.5 Å resolution
    • Lukacs C.M., Kucera R., Schildkraut I., Aggarwal A.K. Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 Å resolution. Nature Struct. Biol. 7:2000;134-140.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 134-140
    • Lukacs, C.M.1    Kucera, R.2    Schildkraut, I.3    Aggarwal, A.K.4
  • 25
    • 0033634983 scopus 로고    scopus 로고
    • Structure of BamHI bound to nonspecific DNA: A model for DNA sliding
    • Viadiu H., Aggarwal A.K. Structure of BamHI bound to nonspecific DNA: a model for DNA sliding. Mol. Cell. 5:2000;889-895.
    • (2000) Mol. Cell , vol.5 , pp. 889-895
    • Viadiu, H.1    Aggarwal, A.K.2
  • 27
    • 0036304570 scopus 로고    scopus 로고
    • Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity
    • Samuelson J.C., Xu S.Y. Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity. J. Mol. Biol. 319:2002;673-683.
    • (2002) J. Mol. Biol. , vol.319 , pp. 673-683
    • Samuelson, J.C.1    Xu, S.Y.2
  • 28
    • 0031717755 scopus 로고    scopus 로고
    • The role of metals in catalysis by the restriction endonuclease BamHI
    • Viadiu H., Aggarwal A.K. The role of metals in catalysis by the restriction endonuclease BamHI. Nature Struct. Biol. 5:1998;910-916.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 910-916
    • Viadiu, H.1    Aggarwal, A.K.2
  • 29
    • 0037180394 scopus 로고    scopus 로고
    • Catalytic mechanisms of restriction and homing endonucleases
    • Galburt E.A., Stoddard B.L. Catalytic mechanisms of restriction and homing endonucleases. Biochemistry. 41:2002;13851-13860.
    • (2002) Biochemistry , vol.41 , pp. 13851-13860
    • Galburt, E.A.1    Stoddard, B.L.2
  • 30
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z. 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
  • 32
    • 0002583957 scopus 로고
    • Dm: An automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newsletter
    • Cowtan K. dm: an automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newsletter. Protein Crystallog. 31:1994;34-38.
    • (1994) Protein Crystallog. , vol.31 , pp. 34-38
    • Cowtan, K.1
  • 33
    • 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 M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
    • (1991) Acta Crystallog. Sect. a , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 35
    • 0030841587 scopus 로고    scopus 로고
    • Electron-density map interpretation
    • Jones T.A., Kjeldgaard M. Electron-density map interpretation. Methods Enzymol. 276:1997;173-207.
    • (1997) Methods Enzymol. , vol.276 , pp. 173-207
    • Jones, T.A.1    Kjeldgaard, M.2
  • 36
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R., Billeter M., Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14:1996;51-55.
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3


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