-
1
-
-
0035883723
-
Structure and function of type II restriction endonucleases
-
A. Pingoud, and A. Jeltsch 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
-
2
-
-
0024294634
-
Crystal structure of trp repressor/operator complex at atomic resolution [published erratum appears in Nature 1988 Oct 27; 335(6193):837]
-
Z. Otwinowski, R.W. Schevitz, R.G. Zhang, C.L. Lawson, A. Joachimiak, R.Q. Marmorstein, B.F. Luisi, and P.B. Sigler Crystal structure of trp repressor/operator complex at atomic resolution [published erratum appears in Nature 1988 Oct 27; 335(6193):837] Nature 335 1988 321 329
-
(1988)
Nature
, vol.335
, pp. 321-329
-
-
Otwinowski, Z.1
Schevitz, R.W.2
Zhang, R.G.3
Lawson, C.L.4
Joachimiak, A.5
Marmorstein, R.Q.6
Luisi, B.F.7
Sigler, P.B.8
-
3
-
-
0032540302
-
Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites
-
A. Bareket-Samish, I. Cohen, and T.E. Haran Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites J. Mol. Biol. 277 1998 1071 1080
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 1071-1080
-
-
Bareket-Samish, A.1
Cohen, I.2
Haran, T.E.3
-
4
-
-
0035900557
-
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: Alteration of DNA binding specificity through alteration of DNA kinking
-
S. Chen, A. Gunasekera, X. Zhang, T.A. Kunkel, R.H. Ebright, and H.M. Berman Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking J. Mol. Biol. 314 2001 75 82
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 75-82
-
-
Chen, S.1
Gunasekera, A.2
Zhang, X.3
Kunkel, T.A.4
Ebright, R.H.5
Berman, H.M.6
-
5
-
-
0023187152
-
Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro
-
G.B. Koudelka, S.C. Harrison, and M. Ptashne Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro Nature 326 1987 886 888
-
(1987)
Nature
, vol.326
, pp. 886-888
-
-
Koudelka, G.B.1
Harrison, S.C.2
Ptashne, M.3
-
6
-
-
0035843172
-
Crystal structures of SarA, a pleiotropic regulator of virulence genes in S. aureus
-
M.A. Schumacher, B.K. Hurlburt, and R.G. Brennan Crystal structures of SarA, a pleiotropic regulator of virulence genes in S. aureus Nature 409 2001 215 219
-
(2001)
Nature
, vol.409
, pp. 215-219
-
-
Schumacher, M.A.1
Hurlburt, B.K.2
Brennan, R.G.3
-
7
-
-
0032972857
-
Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease
-
A.M. Martin, M.D. Sam, N.O. Reich, and J.J. Perona Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease Nature Struct. Biol. 6 1999 269 277
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 269-277
-
-
Martin, A.M.1
Sam, M.D.2
Reich, N.O.3
Perona, J.J.4
-
8
-
-
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 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
-
9
-
-
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 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
-
10
-
-
0029790522
-
Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme
-
A. Jeltsch, C. Wenz, F. Stahl, and A. Pingoud Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme EMBO J. 15 1996 5104 5111
-
(1996)
EMBO J.
, vol.15
, pp. 5104-5111
-
-
Jeltsch, A.1
Wenz, C.2
Stahl, F.3
Pingoud, A.4
-
11
-
-
0019816896
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. the Escherichia coli repressor-operator interaction: Equilibrium measurements
-
R.B. Winter, and P.H. von Hippel Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor-operator interaction: equilibrium measurements Biochemistry 20 1981 6948 6960
-
(1981)
Biochemistry
, vol.20
, pp. 6948-6960
-
-
Winter, R.B.1
Von Hippel, P.H.2
-
12
-
-
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
-
13
-
-
0029943025
-
Simultaneous binding and bending of promoter DNA by the TATA binding protein: Real time kinetic measurements
-
K.M. Parkhurst, M. Brenowitz, and L.J. Parkhurst Simultaneous binding and bending of promoter DNA by the TATA binding protein: real time kinetic measurements Biochemistry 35 1996 7459 7465
-
(1996)
Biochemistry
, vol.35
, pp. 7459-7465
-
-
Parkhurst, K.M.1
Brenowitz, M.2
Parkhurst, L.J.3
-
14
-
-
0346220020
-
Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence
-
D.A. Hiller, J.M. Fogg, A.M. Martin, J.M. Beechem, N.O. Reich, and J.J. Perona Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence Biochemistry 42 2003 14375 14385
-
(2003)
Biochemistry
, vol.42
, pp. 14375-14385
-
-
Hiller, D.A.1
Fogg, J.M.2
Martin, A.M.3
Beechem, J.M.4
Reich, N.O.5
Perona, J.J.6
-
15
-
-
0037451299
-
Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling
-
D.M. Gowers, and S.E. Halford Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling EMBO J. 22 2003 1410 1418
-
(2003)
EMBO J.
, vol.22
, pp. 1410-1418
-
-
Gowers, D.M.1
Halford, S.E.2
-
16
-
-
23444450909
-
Coupling of local folding to site-specific binding of proteins to DNA
-
R.S. Spolar, and M.T. Record Jr Coupling of local folding to site-specific binding of proteins to DNA Science 263 1994 777 784
-
(1994)
Science
, vol.263
, pp. 777-784
-
-
Spolar, R.S.1
Record, M.T.2
-
17
-
-
0034435652
-
Structural and thermodynamic strategies for site-specific DNA binding proteins
-
L. Jen-Jacobson, L.E. Engler, and L.A. Jacobson Structural and thermodynamic strategies for site-specific DNA binding proteins Struct. Fold. Des. 8 2000 1015 1023
-
(2000)
Struct. Fold. Des.
, vol.8
, pp. 1015-1023
-
-
Jen-Jacobson, L.1
Engler, L.E.2
Jacobson, L.A.3
-
18
-
-
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 Nature Struct. Biol. 1 1994 469 475
-
(1994)
Nature 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
-
20
-
-
0028773473
-
Structure of restriction endonuclease BamHI phased at 1.95 Å resolution by MAD analysis
-
M. Newman, T. Strzelecka, L.F. Dorner, 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
Aggarwal, A.K.4
-
21
-
-
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
-
22
-
-
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 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
-
23
-
-
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
-
24
-
-
0031576347
-
Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis
-
J.J. Perona, and A.M. Martin Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis J. Mol. Biol. 273 1997 207 225
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 207-225
-
-
Perona, J.J.1
Martin, A.M.2
-
25
-
-
5144224923
-
2+ binding in the active site of HincII bound to DNA; Implications for the catalytic mechanism
-
2+ binding in the active site of HincII bound to DNA; implications for the catalytic mechanism. Biochemistry, 43, 13256-13270.
-
(2004)
Biochemistry
, vol.43
, pp. 13256-13270
-
-
Etzkorn, C.1
Horton, N.C.2
-
27
-
-
0032473571
-
Structural basis for MutH activation in E-coli mismatch repair and relationship of MutH to restriction endonucleases
-
C. Ban, and W. Yang Structural basis for MutH activation in E-coli mismatch repair and relationship of MutH to restriction endonucleases EMBO J. 17 1998 1526 1534
-
(1998)
EMBO J.
, vol.17
, pp. 1526-1534
-
-
Ban, C.1
Yang, W.2
-
28
-
-
0024531901
-
Facilitated target location in biological systems
-
P.H. von Hippel, and O.G. Berg Facilitated target location in biological systems J. Biol. Chem. 264 1989 675 678
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 675-678
-
-
Von Hippel, P.H.1
Berg, O.G.2
-
29
-
-
0034705029
-
Crystallographic snapshots along a protein-induced DNA-bending pathway
-
N.C. Horton, and J.J. Perona Crystallographic snapshots along a protein-induced DNA-bending pathway Proc. Natl Acad. Sci. USA 97 2000 5729 5734
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 5729-5734
-
-
Horton, N.C.1
Perona, J.J.2
-
30
-
-
0026244229
-
MOLSCRIPT - A program to produce both detailed and schematic plots of protein structures
-
P.J. Kraulis MOLSCRIPT - a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
-
(1991)
J. Appl. Crystallog.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
31
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
C.W. Carter Jr R.M. Sweet Academic Press New York
-
Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode C.W. Carter Jr R.M. Sweet Methods in Enzymology 1997 Academic Press New York 307 326
-
(1997)
Methods in Enzymology
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
32
-
-
0033954256
-
The Protein Data Bank
-
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
-
33
-
-
0032790081
-
XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density
-
D.E. McRee XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
-
(1999)
J. Struct. Biol.
, vol.125
, pp. 156-165
-
-
McRee, D.E.1
-
34
-
-
0033119938
-
Further additions to MolScript version 1.4, including reading and contouring of electron-density maps
-
R.M. Esnouf Further additions to MolScript version 1.4, including reading and contouring of electron-density maps Acta Crystallog. sect. D 55 1999 938 940
-
(1999)
Acta Crystallog. Sect. D
, vol.55
, pp. 938-940
-
-
Esnouf, R.M.1
-
35
-
-
0026244229
-
MOLSCRIPT-a program to produce both detailed and schematic plots of protein structures
-
P.J. Kraulis MOLSCRIPT-a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallog. 24 1991 946 950
-
(1991)
J. Appl. Crystallog.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
36
-
-
0028057108
-
Raster3D version 2.0-a program for photorealistic molecular graphics
-
E.A. Merritt, and M.E.P. Murphy Raster3D version 2.0-a program for photorealistic molecular graphics Acta Crystallog. sect. D 50 1994 869 873
-
(1994)
Acta Crystallog. Sect. D
, vol.50
, pp. 869-873
-
-
Merritt, E.A.1
Murphy, M.E.P.2
-
37
-
-
0033954256
-
The Protein Data Bank
-
H.M. Berman The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
-
38
-
-
0011126038
-
-
SERC Daresbury Laboratory Warrington, UK
-
Collaborative Computing Project No. 4 A Suite of Programs for Protein Crystallography 1979 SERC Daresbury Laboratory Warrington, UK
-
(1979)
A Suite of Programs for Protein Crystallography
-
-
-
39
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
W. Kabsch A solution for the best rotation to relate two sets of vectors Acta Crystallog. sect. A 32 1976 922 923
-
(1976)
Acta Crystallog. Sect. a
, vol.32
, pp. 922-923
-
-
Kabsch, W.1
-
40
-
-
0023927904
-
Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure
-
F.M. Richards, and C.E. Kundrot Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure Proteins: Struct. Funct. Genet. 3 1988 71 84
-
(1988)
Proteins: Struct. Funct. Genet.
, vol.3
, pp. 71-84
-
-
Richards, F.M.1
Kundrot, C.E.2
-
41
-
-
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. Dynam. 6 1988 63 91
-
(1988)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
42
-
-
0024539180
-
Defining the structure of irregular nucleic acids: Conventions and principles
-
R. Lavery, and H. Sklenar Defining the structure of irregular nucleic acids: conventions and principles J. Biomol. Struct. Dynam. 6 1989 655 667
-
(1989)
J. Biomol. Struct. Dynam.
, vol.6
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
43
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Mol. Biol. 55 1971 379 400
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
|