-
1
-
-
0028932881
-
Structure and function of restriction endonucleases
-
A.K. Aggarwal 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
-
2
-
-
0024589458
-
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
-
J. Alves, T. Ruter, R. Geiger, A. Fliess, G. Maass, and A. Pingoud 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
-
3
-
-
0028467168
-
Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV
-
A. Athanasiadis, M. Vlassi, D. Kotsifaki, P.A. Tucker, K.S. Wilson, and M. Kokkinidis 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
-
4
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54 1998 905 921
-
(1998)
Acta Crystallogr. D Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
-
7
-
-
0033613907
-
Genetic analysis of the base-specific contacts of BamHI restriction endonuclease
-
L.F. Dorner, J. Bitinaite, R.D. Whitaker, and I. Schildkraut 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
-
8
-
-
0028303476
-
Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease
-
L.F. Dorner, and I. Schildkraut 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
-
9
-
-
0028989426
-
Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants
-
H. Flores, J. Osuna, J. Heitman, and X. Soberon 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
-
10
-
-
0037180394
-
Catalytic mechanisms of restriction and homing endonucleases
-
E.A. Galburt, and B.L. Stoddard 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
-
11
-
-
0036143789
-
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation
-
N.C. Horton, L.F. Dorner, and J.J. Perona Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation Nat. Struct. Biol. 9 2002 42 47
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 42-47
-
-
Horton, N.C.1
Dorner, L.F.2
Perona, J.J.3
-
12
-
-
0032555574
-
Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts
-
N.C. Horton, and J.J. Perona 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
-
-
84889120137
-
Improved methods for building protein models in electron density maps and the location of errors in these models
-
T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr. A47 1991 110 119
-
(1991)
Acta Crystallogr.
, vol.47
, pp. 110-119
-
-
Jones, T.A.1
Zou, J.Y.2
Cowan, S.W.3
Kjeldgaard, M.4
-
14
-
-
0025187081
-
Refinement of Eco RI endonuclease crystal structure: A revised protein chain tracing
-
Y.C. Kim, J.C. Grable, R. Love, P.J. Greene, and J.M. Rosenberg Refinement of Eco RI 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
Love, R.3
Greene, P.J.4
Rosenberg, J.M.5
-
15
-
-
0018791736
-
A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein
-
A. Klug, A. Jack, M.A. Viswamitra, O. Kennard, Z. Shakked, and T.A. Steitz A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein J. Mol. Biol. 131 1979 669 680
-
(1979)
J. Mol. Biol.
, vol.131
, pp. 669-680
-
-
Klug, A.1
Jack, A.2
Viswamitra, M.A.3
Kennard, O.4
Shakked, Z.5
Steitz, T.A.6
-
16
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
Koradi, R., Billeter, M., and Wuthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wuthrich, K.3
-
17
-
-
0034026486
-
On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: A case study employing EcoRV as the target
-
T. Lanio, A. Jeltsch, and A. Pingoud 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
-
19
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
-
R. Lavery, and H. Sklenar The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids J. Biomol. Struct. Dyn. 6 1988 63 91
-
(1988)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
20
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
X.J. Lu, and W.K. Olson 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Res. 31 2003 5108 5121
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5108-5121
-
-
Lu, X.J.1
Olson, W.K.2
-
22
-
-
0033981010
-
Understanding the immutability of restriction enzymes: Crystal structure of BglII and its DNA substrate at 1.5 Å resolution
-
C.M. Lukacs, R. Kucera, I. Schildkraut, and A.K. Aggarwal Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 Å resolution Nat. Struct. Biol. 7 2000 134 140
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 134-140
-
-
Lukacs, C.M.1
Kucera, R.2
Schildkraut, I.3
Aggarwal, A.K.4
-
23
-
-
0035147490
-
Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease
-
C.M. Lukacs, R. Kucera, I. Schildkraut, and A.K. Aggarwal Structure of free BglII reveals an unprecedented scissor-like motion for opening an endonuclease Nat. Struct. Biol. 8 2001 126 130
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 126-130
-
-
Lukacs, C.M.1
Kucera, R.2
Schildkraut, I.3
Aggarwal, A.K.4
-
24
-
-
0028298842
-
Structure of restriction endonuclease BamHI and its relationship to EcoRI
-
M. Newman, T. Strzelecka, L.F. Dorner, I. Schildkraut, and A.K. Aggarwal 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
-
25
-
-
0028773473
-
Structure of restriction endonuclease BamHI phased at 1.95 Å resolution by MAD analysis
-
M. Newman, T. Strzelecka, L.F. Dorner, I. Schildkraut, and A.K. Aggarwal 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
-
26
-
-
0029048413
-
Structure of BamHI endonuclease bound to DNA: Partial folding and unfolding on DNA binding
-
M. Newman, T. Strzelecka, L.F. Dorner, I. Schildkraut, and A.K. Aggarwal 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
-
27
-
-
0025925029
-
Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: Single and double amino acid replacements retaining methyltransferase- sensitive activities
-
J. Osuna, H. Flores, and X. Soberon Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: single and double amino acid replacements retaining methyltransferase-sensitive activities Gene 106 1991 7 12
-
(1991)
Gene
, vol.106
, pp. 7-12
-
-
Osuna, J.1
Flores, H.2
Soberon, X.3
-
28
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Z. Otwinowski 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
-
29
-
-
0035883723
-
Structure and function of type II restriction endonucleases
-
A. Pingoud, and A. Jeltsch Structure and function of type II restriction endonucleases Nucleic Acids Res. 29 2001 3705 3727
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 3705-3727
-
-
Pingoud, A.1
Jeltsch, A.2
-
30
-
-
0037134458
-
Evolutionary relationship between different subgroups of restriction endonucleases
-
V. Pingoud, E. Kubareva, G. Stengel, P. Friedhoff, J.M. Bujnicki, C. Urbanke, A. Sudina, and A. Pingoud Evolutionary relationship between different subgroups of restriction endonucleases J. Biol. Chem. 277 2002 14306 14314
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 14306-14314
-
-
Pingoud, V.1
Kubareva, E.2
Stengel, G.3
Friedhoff, P.4
Bujnicki, J.M.5
Urbanke, C.6
Sudina, A.7
Pingoud, A.8
-
31
-
-
0002598414
-
Type II restriction endonucleases
-
R.J. Roberts Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
-
R.J. Roberts, and S.E. Halford Type II restriction endonucleases R.J. Roberts Nucleases 1993 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
-
(1993)
Nucleases
-
-
Roberts, R.J.1
Halford, S.E.2
-
33
-
-
0036304570
-
Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity
-
J.C. Samuelson, and S.-Y. Xu 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
-
35
-
-
0032533367
-
Protein engineering of the restriction endonuclease EcoRV: Structure-guided design of enzyme variants that recognize the base pairs flanking the recognition site
-
S. Schottler, C. Wenz, T. Lanio, A. Jeltsch, and A. Pingoud 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
-
36
-
-
4143097044
-
Isolation and characterization of new homing endonuclease specificities at individual target site positions
-
D. Sussman, M. Chadsey, S. Fauce, A. Engel, A. Bruett, R. Monnat Jr., B.L. Stoddard, and L.M. Seligman Isolation and characterization of new homing endonuclease specificities at individual target site positions J. Mol. Biol. 342 2004 31 41
-
(2004)
J. Mol. Biol.
, vol.342
, pp. 31-41
-
-
Sussman, D.1
Chadsey, M.2
Fauce, S.3
Engel, A.4
Bruett, A.5
Monnat Jr., R.6
Stoddard, B.L.7
Seligman, L.M.8
-
37
-
-
1942425560
-
Crystal structure of BstYI at 1.85 Å resolution: A thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII
-
S.A. Townson, J.C. Samuelson, E.S. Vanamee, T.A. Edwards, C.R. Escalante, S.-Y. Xu, and A.K. Aggarwal Crystal structure of BstYI at 1.85 Å resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII J. Mol. Biol. 338 2004 725 733
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 725-733
-
-
Townson, S.A.1
Samuelson, J.C.2
Vanamee, E.S.3
Edwards, T.A.4
Escalante, C.R.5
Xu, S.-Y.6
Aggarwal, A.K.7
-
38
-
-
0035096078
-
Restriction enzyme BsoBI-DNA complex: A tunnel for recognition of degenerate DNA sequences and potential histidine catalysis
-
M.J. van der Woerd, J.J. Pelletier, S.-Y. Xu, and A.M. Friedman 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.-Y.3
Friedman, A.M.4
-
39
-
-
0027439390
-
Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin
-
G.D. Van Duyne, R.F. Standaert, P.A. Karplus, S.L. Schreiber, and J. Clardy Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin J. Mol. Biol. 229 1993 105 124
-
(1993)
J. Mol. Biol.
, vol.229
, pp. 105-124
-
-
Van Duyne, G.D.1
Standaert, R.F.2
Karplus, P.A.3
Schreiber, S.L.4
Clardy, J.5
-
40
-
-
18944363746
-
Metal-dependent type II restriction endonucleases
-
A. Messerschmidt W. Bode M. Cygler John Wiley & Sons Chichester, UK
-
E.S. Vanamee, and A.K. Aggarwal Metal-dependent type II restriction endonucleases A. Messerschmidt W. Bode M. Cygler Handbook of Metalloproteins Volume 3 2004 John Wiley & Sons Chichester, UK 742 756
-
(2004)
Handbook of Metalloproteins Volume 3
, pp. 742-756
-
-
Vanamee, E.S.1
Aggarwal, A.K.2
-
41
-
-
18944390568
-
"Two of a Kind": BamHI and BglII
-
A. Pingoud Springer-Verlag Berlin, Heidelberg
-
E.S. Vanamee, H. Viadiu, C.M. Lukacs, and A.K. Aggarwal "Two of A Kind": BamHI and BglII A. Pingoud Nucleic Acids and Molecular Biology, Volume 14 2004 Springer-Verlag Berlin, Heidelberg 215 236
-
(2004)
Nucleic Acids and Molecular Biology, Volume 14
, pp. 215-236
-
-
Vanamee, E.S.1
Viadiu, H.2
Lukacs, C.M.3
Aggarwal, A.K.4
-
42
-
-
0031717755
-
The role of metals in catalysis by the restriction endonuclease BamHI
-
H. Viadiu, and A.K. Aggarwal The role of metals in catalysis by the restriction endonuclease BamHI Nat. Struct. Biol. 5 1998 910 916
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 910-916
-
-
Viadiu, H.1
Aggarwal, A.K.2
-
43
-
-
0033634983
-
Structure of BamHI bound to nonspecific DNA: A model for DNA sliding
-
H. Viadiu, and A.K. Aggarwal 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
-
44
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
A.C. Wallace, R.A. Laskowski, and J.M. Thornton LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8 1995 127 134
-
(1995)
Protein Eng.
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
45
-
-
0032562147
-
Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site
-
C. Wenz, M. Hahn, and A. Pingoud 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
-
46
-
-
0033614013
-
A mutant of BamHI restriction endonuclease which requires N6-methyladenine for cleavage
-
R.D. Whitaker, L.F. Dorner, and I. Schildkraut A mutant of BamHI restriction endonuclease which requires N6-methyladenine for cleavage J. Mol. Biol. 285 1999 1525 1536
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 1525-1536
-
-
Whitaker, R.D.1
Dorner, L.F.2
Schildkraut, I.3
-
47
-
-
0027159254
-
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
-
F.K. Winkler, D.W. Banner, C. Oefner, D. Tsernoglou, R.S. Brown, S.P. Heathman, R.K. Bryan, P.D. Martin, K. Petratos, and K.S. Wilson 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, C.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
-
48
-
-
0025865885
-
Isolation of BamHI variants with reduced cleavage activities
-
S.-Y. Xu, and I. Schildkraut 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
|