-
1
-
-
0030911133
-
Recognition and cleavage of DNA by type-II restriction endonucleases
-
Pingoud A, Jeltsch A Recognition and cleavage of DNA by type-II restriction endonucleases. Eur J Biochem. 246:1997;1-22.
-
(1997)
Eur J Biochem
, vol.246
, pp. 1-22
-
-
Pingoud, A.1
Jeltsch, A.2
-
3
-
-
0000001528
-
Metal activation of enzymes in nucleic acid biochemistry
-
Cowan JA Metal activation of enzymes in nucleic acid biochemistry. Chem Rev. 98:1998;1067-1087.
-
(1998)
Chem Rev
, vol.98
, pp. 1067-1087
-
-
Cowan, J.A.1
-
4
-
-
0028298842
-
Structure of restriction endonuclease BamHI and its relationship to EcoRI
-
Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK 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
-
5
-
-
0025187081
-
Refinement of EcoRI endonuclease crystal structure: A revised protein chain tracing
-
Kim YC, Grable JC, Choi PJ, Greene P, Rosenberg JM Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science. 249:1990;1307-1309.
-
(1990)
Science
, vol.249
, pp. 1307-1309
-
-
Kim, Y.C.1
Grable, J.C.2
Choi, P.J.3
Greene, P.4
Rosenberg, J.M.5
-
6
-
-
0029995002
-
Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 Å resolution
-
Bozic D, Grazulis S, Siksnys V, Huber R Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 Å resolution. J Mol Biol. 255:1996;176-186.
-
(1996)
J Mol Biol
, vol.255
, pp. 176-186
-
-
Bozic, D.1
Grazulis, S.2
Siksnys, V.3
Huber, R.4
-
7
-
-
0027159254
-
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
-
Winkler FK, Banner DW, Oefner D, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1993;1781-1795.
-
(1993)
EMBO J
, vol.12
, pp. 1781-1795
-
-
Winkler, F.K.1
Banner, D.W.2
Oefner, D.3
Tsernoglou, D.4
Brown, R.S.5
Heathman, S.P.6
Bryan, R.K.7
Martin, P.D.8
Petratos, K.9
Wilson, K.S.10
-
8
-
-
0028467168
-
Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV
-
Athanasiadis A, Vlassi M, Kotsifaki D, Tucker PA, Wilson KS, Kokkinidis M Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Nat Struct Biol. 1:1994;469-475.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 469-475
-
-
Athanasiadis, A.1
Vlassi, M.2
Kotsifaki, D.3
Tucker, P.A.4
Wilson, K.S.5
Kokkinidis, M.6
-
10
-
-
0032530311
-
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence
-
2+ and reveals two metals bound at the active site, leading the authors to propose a two-metal mechanism of cleavage
-
2+ and reveals two metals bound at the active site, leading the authors to propose a two-metal mechanism of cleavage.
-
(1998)
EMBO J
, vol.17
, pp. 5466-5476
-
-
Newman, M.1
Lunnen, K.2
Wilson, G.3
Greci, J.4
Schildkraut, I.5
Phillips, S.E.V.6
-
11
-
-
0028172810
-
Five-stranded β-sheet with two α-helices: A structural link between restriction endonucleases EcoRI and EcoRV
-
Venclovas C, Timinskas A, Siksnys V Five-stranded β-sheet with two α-helices: a structural link between restriction endonucleases EcoRI and EcoRV. Proteins. 20:1994;279-282.
-
(1994)
Proteins
, vol.20
, pp. 279-282
-
-
Venclovas, C.1
Timinskas, A.2
Siksnys, V.3
-
12
-
-
0032473571
-
Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases
-
The crystal structure of MutH, a protein involved in methyl-directed DNA mismatch repair in Escherichia coli, is remarkably similar to the type II restriction endonuclease PvuII
-
Ban C, Yang W Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases. EMBO J. 17:1998;1526-1534. The crystal structure of MutH, a protein involved in methyl-directed DNA mismatch repair in Escherichia coli, is remarkably similar to the type II restriction endonuclease PvuII.
-
(1998)
EMBO J
, vol.17
, pp. 1526-1534
-
-
Ban, C.1
Yang, W.2
-
13
-
-
0030790696
-
Structure of the multimodular endonuclease FokI bound to DNA
-
Wah DA, Hirsch JA, Dorner LF, Schildkraut I, Aggarwal AK Structure of the multimodular endonuclease FokI bound to DNA. Nature. 388:1997;97-100.
-
(1997)
Nature
, vol.388
, pp. 97-100
-
-
Wah, D.A.1
Hirsch, J.A.2
Dorner, L.F.3
Schildkraut, I.4
Aggarwal, A.K.5
-
14
-
-
0032493296
-
Structural, functional, and evolutionary relationships between λ-exonuclease and the type II restriction endonucleases
-
In an extension of the original crystal structure determination, which unexpectedly revealed λ-exonuclease to be structurally similar to the type II endonucleases, the authors provide an in-depth analysis of the regions of structural similarity
-
Kovall RA, Matthews BW Structural, functional, and evolutionary relationships between λ-exonuclease and the type II restriction endonucleases. Proc Natl Acad Sci USA. 95:1998;7893-7897. In an extension of the original crystal structure determination, which unexpectedly revealed λ-exonuclease to be structurally similar to the type II endonucleases, the authors provide an in-depth analysis of the regions of structural similarity.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 7893-7897
-
-
Kovall, R.A.1
Matthews, B.W.2
-
15
-
-
0021228511
-
The stereochemical course of the restriction enzyme EcoRI-catalysed reaction
-
Connolly BA, Eckstein F, Pingoud A The stereochemical course of the restriction enzyme EcoRI-catalysed reaction. J Biol Chem. 259:1984;10760-10763.
-
(1984)
J Biol Chem
, vol.259
, pp. 10760-10763
-
-
Connolly, B.A.1
Eckstein, F.2
Pingoud, A.3
-
16
-
-
0026687132
-
Stereochemical outcome of the hydrolysis reaction catalyzed by the EcoRV restriction endonuclease
-
Grasby JA, Connolly BA Stereochemical outcome of the hydrolysis reaction catalyzed by the EcoRV restriction endonuclease. Biochemistry. 31:1992;7855-7861.
-
(1992)
Biochemistry
, vol.31
, pp. 7855-7861
-
-
Grasby, J.A.1
Connolly, B.A.2
-
17
-
-
0023057187
-
Site-directed mutagenesis experiments suggest that Glu111, Glu144 and Arg145 are essential for endonucleolytic activity of EcoRI
-
Wolfes H, Alves J, Fliess A, Geiger R, Pingoud A Site-directed mutagenesis experiments suggest that Glu111, Glu144 and Arg145 are essential for endonucleolytic activity of EcoRI. Nucleic Acids Res. 14:1986;9063-9080.
-
(1986)
Nucleic Acids Res
, vol.14
, pp. 9063-9080
-
-
Wolfes, H.1
Alves, J.2
Fliess, A.3
Geiger, R.4
Pingoud, A.5
-
18
-
-
0024359479
-
The negative charge of Glu111 is required to activate the cleavage center of EcoRI endonuclease
-
Wright DJ, King K, Modrich P The negative charge of Glu111 is required to activate the cleavage center of EcoRI endonuclease. J Biol Chem. 264:1989;11816-11821.
-
(1989)
J Biol Chem
, vol.264
, pp. 11816-11821
-
-
Wright, D.J.1
King, K.2
Modrich, P.3
-
19
-
-
0024379261
-
Glu111 is required for activation of the DNA cleavage center of EcoRI endonuclease
-
King K, Benkovic SJ, Modrich P Glu111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J Biol Chem. 264:1989;11807-11815.
-
(1989)
J Biol Chem
, vol.264
, pp. 11807-11815
-
-
King, K.1
Benkovic, S.J.2
Modrich, P.3
-
20
-
-
0025865885
-
Isolation of BamHI variants with reduced cleavage activities
-
Xu SY, Schildkraut I Isolation of BamHI variants with reduced cleavage activities. J Biol Chem. 266:1991;4425-4429.
-
(1991)
J Biol Chem
, vol.266
, pp. 4425-4429
-
-
Xu, S.Y.1
Schildkraut, I.2
-
21
-
-
0026696177
-
A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV
-
Selent U, Ruter T, Kohler E, Liedtke M, Thielking V, Alves J, Oelgeschlager T, Wolfes H, Peters F, Pingoud A A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV. Biochemistry. 31:1992;4808-4815.
-
(1992)
Biochemistry
, vol.31
, pp. 4808-4815
-
-
Selent, U.1
Ruter, T.2
Kohler, E.3
Liedtke, M.4
Thielking, V.5
Alves, J.6
Oelgeschlager, T.7
Wolfes, H.8
Peters, F.9
Pingoud, A.10
-
22
-
-
0028303476
-
Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease
-
Dorner LF, Schildkraut I Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease. Nucleic Acids Res. 22:1994;1068-1074.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 1068-1074
-
-
Dorner, L.F.1
Schildkraut, I.2
-
23
-
-
0029063469
-
Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI
-
Grabowski G, Jeltsch A, Wolfes H, Maass G, Alves J Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI. Gene. 157:1995;113-118.
-
(1995)
Gene
, vol.157
, pp. 113-118
-
-
Grabowski, G.1
Jeltsch, A.2
Wolfes, H.3
Maass, G.4
Alves, J.5
-
24
-
-
0030867835
-
Catalytic and DNA binding properties of PvuII restriction endonuclease mutants
-
Nastri HG, Evans PD, Walker IH, Riggs PD Catalytic and DNA binding properties of PvuII restriction endonuclease mutants. J Biol Chem. 272:1997;25761-25767.
-
(1997)
J Biol Chem
, vol.272
, pp. 25761-25767
-
-
Nastri, H.G.1
Evans, P.D.2
Walker, I.H.3
Riggs, P.D.4
-
25
-
-
0032486108
-
Structure based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues
-
The authors show that Glu204 rather than Ser188 is part of the catalytic triad of Cfr10I, demonstrating the importance of spatial versus sequence conservation in the formation of the active site of restriction endonucleases
-
Skirgaila R, Grazulis S, Bozic D, Huber R, Siksnys V Structure based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues. J Mol Biol. 279:1998;473-481. The authors show that Glu204 rather than Ser188 is part of the catalytic triad of Cfr10I, demonstrating the importance of spatial versus sequence conservation in the formation of the active site of restriction endonucleases.
-
(1998)
J Mol Biol
, vol.279
, pp. 473-481
-
-
Skirgaila, R.1
Grazulis, S.2
Bozic, D.3
Huber, R.4
Siksnys, V.5
-
26
-
-
0027218657
-
Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes
-
Jeltsch A, Alves J, Wolfes H, Maass G, Pingoud A Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes. Proc Natl Acad Sci USA. 90:1993;8499-8503.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 8499-8503
-
-
Jeltsch, A.1
Alves, J.2
Wolfes, H.3
Maass, G.4
Pingoud, A.5
-
27
-
-
0028988416
-
2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 Å resolution
-
2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry. 34:1995;683-696.
-
(1995)
Biochemistry
, vol.34
, pp. 683-696
-
-
Kostrewa, D.1
Winkler, F.K.2
-
28
-
-
0028938496
-
Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases
-
Vipond IB, Baldwin GS, Halford SE Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases. Biochemistry. 34:1995;697-704.
-
(1995)
Biochemistry
, vol.34
, pp. 697-704
-
-
Vipond, I.B.1
Baldwin, G.S.2
Halford, S.E.3
-
29
-
-
0032506110
-
Metal ion-mediated substrate assisted catalysis in type II restriction endonucleases
-
The structure of the protein-DNA complex of the EcoRV mutant T93A reveals two metals bound at the active site, one of which is in a distinct location that has not been seen in any of the previously determined structures of EcoRV. The authors propose a novel three-metal mechanism of catalysis, on the basis of this mutant structure
-
Horton NC, Newberry KJ, Perona JJ Metal ion-mediated substrate assisted catalysis in type II restriction endonucleases. Proc Natl Acad Sci USA. 95:1998;13489-13494. The structure of the protein-DNA complex of the EcoRV mutant T93A reveals two metals bound at the active site, one of which is in a distinct location that has not been seen in any of the previously determined structures of EcoRV. The authors propose a novel three-metal mechanism of catalysis, on the basis of this mutant structure.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 13489-13494
-
-
Horton, N.C.1
Newberry, K.J.2
Perona, J.J.3
-
30
-
-
0031717755
-
The role of metals in catalysis by the restriction endonuclease BamHI
-
2+ where the DNA has been cleaved in the crystal. From these structures the authors propose a two-metal mechanism of cleavage very similar to the one proposed for the 3′→5′ exonuclease domain of E. coli DNA polymerase I
-
2+ where the DNA has been cleaved in the crystal. From these structures the authors propose a two-metal mechanism of cleavage very similar to the one proposed for the 3′→5′ exonuclease domain of E. coli DNA polymerase I.
-
(1998)
Nat Struct Biol
, vol.5
, pp. 910-916
-
-
Viadiu, H.1
Aggarwal, A.K.2
-
31
-
-
0030886344
-
Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage?
-
Groll DH, Jeltsch A, Selent U, Pingoud A Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage? Biochemistry. 36:1997;11389-11401.
-
(1997)
Biochemistry
, vol.36
, pp. 11389-11401
-
-
Groll, D.H.1
Jeltsch, A.2
Selent, U.3
Pingoud, A.4
-
32
-
-
0033597347
-
DNA cleavage by the EcoRV restriction endonuclease: Roles of divalent metal ions in specificity and catalysis
-
2+. The results support a two-metal mechanism in which a water molecule bound to metal B (ligated to the sidechains of Asp74 and Glu45) is in an appropriate position for in-line attack of the scissile phosphate
-
2+. The results support a two-metal mechanism in which a water molecule bound to metal B (ligated to the sidechains of Asp74 and Glu45) is in an appropriate position for in-line attack of the scissile phosphate.
-
(1999)
J Mol Biol
, vol.288
, pp. 87-103
-
-
Baldwin, G.S.1
Sessions, R.B.2
Erskine, S.G.3
Halford, S.E.4
-
33
-
-
0033597317
-
DNA cleavage by the EcoRV restriction endonuclease: PH dependence and proton transfers in catalysis
-
On the basis of the pH dependence of the cleavage reaction for wildtype EcoRV and for the mutant D36E, cleavage for wildtype EcoRV requires the deprotonation of two acidic groups whereas mutant D36E requires only a single deprotonation event. This implicates Asp36 as a participant in the catalytic mechanism
-
Stanford NP, Halford SE, Baldwin GS DNA cleavage by the EcoRV restriction endonuclease: pH dependence and proton transfers in catalysis. J Mol Biol. 288:1999;105-116. On the basis of the pH dependence of the cleavage reaction for wildtype EcoRV and for the mutant D36E, cleavage for wildtype EcoRV requires the deprotonation of two acidic groups whereas mutant D36E requires only a single deprotonation event. This implicates Asp36 as a participant in the catalytic mechanism.
-
(1999)
J Mol Biol
, vol.288
, pp. 105-116
-
-
Stanford, N.P.1
Halford, S.E.2
Baldwin, G.S.3
-
34
-
-
0029991992
-
Influence of the phosphate backbone on the recognition and hydrolysis of DNA by the EcoRV restriction endonuclease
-
Thorogood H, Grasby JA, Connolly BA Influence of the phosphate backbone on the recognition and hydrolysis of DNA by the EcoRV restriction endonuclease. J Biol Chem. 271:1996;8855-8862.
-
(1996)
J Biol Chem
, vol.271
, pp. 8855-8862
-
-
Thorogood, H.1
Grasby, J.A.2
Connolly, B.A.3
-
35
-
-
0026019625
-
Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two-metal ion mechanism
-
Beese LS, Steitz TA Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two-metal ion mechanism. EMBO J. 10:1991;25-33.
-
(1991)
EMBO J
, vol.10
, pp. 25-33
-
-
Beese, L.S.1
Steitz, T.A.2
-
36
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis PJ MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr. 24:1991;946-950.
-
(1991)
J Appl Crystallogr
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
|