-
1
-
-
46349101158
-
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
-
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.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 3552-3569
-
-
Orlowski, J.1
Bujnicki, J.M.2
-
2
-
-
0035883723
-
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.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 3705-3727
-
-
Pingoud, A.1
Jeltsch, A.2
-
3
-
-
34247863978
-
Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically
-
Kaus-Drobek, M., Czapinska, H., Sokolowska, M., Tamulaitis, G., Szczepanowski, R.H., Urbanke, C., Siksnys, V. and Bochtler, M. (2007) Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically. Nucleic Acids Res., 35, 2035-2046.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 2035-2046
-
-
Kaus-Drobek, M.1
Czapinska, H.2
Sokolowska, M.3
Tamulaitis, G.4
Szczepanowski, R.H.5
Urbanke, C.6
Siksnys, V.7
Bochtler, M.8
-
4
-
-
34248153723
-
Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA
-
Sokolowska, M., Kaus-Drobek, M., Czapinska, H., Tamulaitis, G., Szczepanowski, R.H., Urbanke, C., Siksnys, V. and Bochtler, M. (2007) Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. J. Mol. Biol., 369, 722-734.
-
(2007)
J. Mol. Biol.
, vol.369
, pp. 722-734
-
-
Sokolowska, M.1
Kaus-Drobek, M.2
Czapinska, H.3
Tamulaitis, G.4
Szczepanowski, R.H.5
Urbanke, C.6
Siksnys, V.7
Bochtler, M.8
-
5
-
-
4444373591
-
An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site
-
Xu, Q.S., Kucera, R.B., Roberts, R.J. and Guo, H.C. (2004) An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure, 12, 1741-1747.
-
(2004)
Structure
, vol.12
, pp. 1741-1747
-
-
Xu, Q.S.1
Kucera, R.B.2
Roberts, R.J.3
Guo, H.C.4
-
6
-
-
0028172810
-
Five-stranded beta-sheet sandwiched with two alpha-helices: A structural link between restriction endonucleases EcoRI and EcoRV
-
Venclovas, C., Timinskas, A. and Siksnys, V. (1994) Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV. Proteins, 20, 279-282.
-
(1994)
Proteins
, vol.20
, pp. 279-282
-
-
Venclovas, C.1
Timinskas, A.2
Siksnys, V.3
-
7
-
-
34249862289
-
Topology of Type II REases revisited; Structural classes and the common conserved core
-
Niv, M.Y., Ripoll, D.R., Vila, J.A., Liwo, A., Vanamee, E.S., Aggarwal, A.K., Weinstein, H. and Scheraga, H.A. (2007) Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Res., 35, 2227-2237.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 2227-2237
-
-
Niv, M.Y.1
Ripoll, D.R.2
Vila, J.A.3
Liwo, A.4
Vanamee, E.S.5
Aggarwal, A.K.6
Weinstein, H.7
Scheraga, H.A.8
-
8
-
-
70349229163
-
On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family
-
Pingoud, V., Wende, W., Friedhoff, P., Reuter, M., Alves, J., Jeltsch, A., Mones, L., Fuxreiter, M. and Pingoud, A. (2009) On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J. Mol. Biol., 393, 140-160.
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 140-160
-
-
Pingoud, V.1
Wende, W.2
Friedhoff, P.3
Reuter, M.4
Alves, J.5
Jeltsch, A.6
Mones, L.7
Fuxreiter, M.8
Pingoud, A.9
-
9
-
-
55549123481
-
An equivalent metal ion in one- and two-metal-ion catalysis
-
Yang, W. (2008) An equivalent metal ion in one- and two-metal-ion catalysis. Nat. Struct. Mol. Biol., 15, 1228-1231.
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 1228-1231
-
-
Yang, W.1
-
10
-
-
77952542578
-
Nucleophile activation in PD. . .(D/E)xK metallonucleases: An experimental and computational pK(a) study
-
Xie, F., Briggs, J.M. and Dupureur, C.M. (2010) Nucleophile activation in PD. . .(D/E)xK metallonucleases: an experimental and computational pK(a) study. J. Inorg. Biochem.
-
(2010)
J. Inorg. Biochem
-
-
Xie, F.1
Briggs, J.M.2
Dupureur, C.M.3
-
11
-
-
0037180394
-
Catalytic mechanisms of restriction and homing endonucleases
-
Galburt, E.A. and Stoddard, B.L. (2002) Catalytic mechanisms of restriction and homing endonucleases. Biochemistry, 41, 13851-13860.
-
(2002)
Biochemistry
, vol.41
, pp. 13851-13860
-
-
Galburt, E.A.1
Stoddard, B.L.2
-
12
-
-
67649888360
-
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
-
13
-
-
77953604755
-
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI
-
Shen, B.W., Heiter, D.F., Chan, S.H., Wang, H., Xu, S.Y., Morgan, R.D., Wilson, G.G. and Stoddard, B.L. (2010) Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. Structure, 18, 734-743.
-
(2010)
Structure
, vol.18
, pp. 734-743
-
-
Shen, B.W.1
Heiter, D.F.2
Chan, S.H.3
Wang, H.4
Xu, S.Y.5
Morgan, R.D.6
Wilson, G.G.7
Stoddard, B.L.8
-
14
-
-
20144386860
-
Structural insights into the first incision reaction during nucleotide excision repair
-
Truglio, J.J., Rhau, B., Croteau, D.L., Wang, L., Skorvaga, M., Karakas, E., DellaVecchia, M.J., Wang, H., Van Houten, B. and Kisker, C. (2005) Structural insights into the first incision reaction during nucleotide excision repair. EMBO J., 24, 885-894.
-
(2005)
EMBO J.
, vol.24
, pp. 885-894
-
-
Truglio, J.J.1
Rhau, B.2
Croteau, D.L.3
Wang, L.4
Skorvaga, M.5
Karakas, E.6
Dellavecchia, M.J.7
Wang, H.8
Van Houten, B.9
Kisker, C.10
-
15
-
-
0035151431
-
Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles
-
Bujnicki, J.M. and Rychlewski, L. (2001) Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles. J. Mol. Microbiol. Biotechnol., 3, 69-72.
-
(2001)
J. Mol. Microbiol. Biotechnol.
, vol.3
, pp. 69-72
-
-
Bujnicki, J.M.1
Rychlewski, L.2
-
16
-
-
0028024850
-
Structure of PvuII endonuclease with cognate DNA
-
Cheng, X., Balendiran, K., Schildkraut, I. and Anderson, J.E. (1994) Structure of PvuII endonuclease with cognate DNA. EMBO J., 13, 3927-3935.
-
(1994)
EMBO J.
, vol.13
, pp. 3927-3935
-
-
Cheng, X.1
Balendiran, K.2
Schildkraut, I.3
Anderson, J.E.4
-
17
-
-
0029048413
-
Structure of Bam HI endonuclease bound to DNA: Partial folding and unfolding on DNA binding
-
Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I. and Aggarwal, A.K. (1995) Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science, 269, 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
-
18
-
-
0033981010
-
Understanding the immutability of restriction enzymes: Crystal structure of BglII and its DNA substrate at 1.5 A resolution
-
Lukacs, C.M., Kucera, R., Schildkraut, I. and Aggarwal, A.K. (2000) Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Nat. Struct. Biol., 7, 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
-
19
-
-
41449117713
-
Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding
-
Lambert, A.R., Sussman, D., Shen, B., Maunus, R., Nix, J., Samuelson, J., Xu, S.Y. and Stoddard, B.L. (2008) Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure, 16, 558-569.
-
(2008)
Structure
, vol.16
, pp. 558-569
-
-
Lambert, A.R.1
Sussman, D.2
Shen, B.3
Maunus, R.4
Nix, J.5
Samuelson, J.6
Xu, S.Y.7
Stoddard, B.L.8
-
20
-
-
14044252836
-
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA
-
Hashimoto, H., Shimizu, T., Imasaki, T., Kato, M., Shichijo, N., Kita, K. and Sato, M. (2005) Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA. J. Biol. Chem., 280, 5605-5610.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 5605-5610
-
-
Hashimoto, H.1
Shimizu, T.2
Imasaki, T.3
Kato, M.4
Shichijo, N.5
Kita, K.6
Sato, M.7
-
21
-
-
0033818703
-
Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA
-
Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V. and Huber, R. (2000) Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat. Struct. Biol., 7, 792-799.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 792-799
-
-
Deibert, M.1
Grazulis, S.2
Sasnauskas, G.3
Siksnys, V.4
Huber, R.5
-
22
-
-
33646813662
-
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease
-
Bochtler, M., Szczepanowski, R.H., Tamulaitis, G., Grazulis, S., Czapinska, H., Manakova, E. and Siksnys, V. (2006) Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J., 25, 2219-2229.
-
(2006)
EMBO J.
, vol.25
, pp. 2219-2229
-
-
Bochtler, M.1
Szczepanowski, R.H.2
Tamulaitis, G.3
Grazulis, S.4
Czapinska, H.5
Manakova, E.6
Siksnys, V.7
-
23
-
-
0029975922
-
Probing the indirect readout of the restriction enzyme EcoRV. Mutational analysis of contacts to the DNA backbone
-
Wenz, C., Jeltsch, A. and Pingoud, A. (1996) Probing the indirect readout of the restriction enzyme EcoRV. Mutational analysis of contacts to the DNA backbone. J. Biol. Chem., 271, 5565-5573.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 5565-5573
-
-
Wenz, C.1
Jeltsch, A.2
Pingoud, A.3
-
24
-
-
0027159254
-
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
-
Winkler, F.K., Banner, D.W., Oefner, C., Tsernoglou, D., Brown, R.S., Heathman, S.P., Bryan, R.K., Martin, P.D., Petratos, K. and Wilson, K.S. (1993) The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J., 12, 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
-
25
-
-
0032972857
-
Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease
-
Martin, A.M., Sam, M.D., Reich, N.O. and Perona, J.J. (1999) Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease. Nat. Struct. Biol., 6, 269-277.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 269-277
-
-
Martin, A.M.1
Sam, M.D.2
Reich, N.O.3
Perona, J.J.4
-
26
-
-
0036143789
-
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation
-
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.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 42-47
-
-
Horton, N.C.1
Dorner, L.F.2
Perona, J.J.3
-
27
-
-
57049101786
-
Early interrogation and recognition of DNA sequence by indirect readout
-
Little, E.J., Babic, A.C. and Horton, N.C. (2008) Early interrogation and recognition of DNA sequence by indirect readout. Structure, 16, 1828-1837.
-
(2008)
Structure
, vol.16
, pp. 1828-1837
-
-
Little, E.J.1
Babic, A.C.2
Horton, N.C.3
-
28
-
-
52049096406
-
DNA distortion and specificity in a sequence-specific endonuclease
-
Babic, A.C., Little, E.J., Manohar, V.M., Bitinaite, J. and Horton, N.C. (2008) DNA distortion and specificity in a sequence-specific endonuclease. J. Mol. Biol., 383, 186-204.
-
(2008)
J. Mol. Biol.
, vol.383
, pp. 186-204
-
-
Babic, A.C.1
Little, E.J.2
Manohar, V.M.3
Bitinaite, J.4
Horton, N.C.5
-
29
-
-
33747689885
-
Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism
-
Joshi, H.K., Etzkorn, C., Chatwell, L., Bitinaite, J. and Horton, N.C. (2006) Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism. J. Biol. Chem., 281, 23852-23869.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 23852-23869
-
-
Joshi, H.K.1
Etzkorn, C.2
Chatwell, L.3
Bitinaite, J.4
Horton, N.C.5
-
30
-
-
56049121435
-
Central base pair flipping and discrimination by PspGI
-
Szczepanowski, R.H., Carpenter, M.A., Czapinska, H., Zaremba, M., Tamulaitis, G., Siksnys, V., Bhagwat, A.S. and Bochtler, M. (2008) Central base pair flipping and discrimination by PspGI. Nucleic Acids Res., 36, 6109-6117.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 6109-6117
-
-
Szczepanowski, R.H.1
Carpenter, M.A.2
Czapinska, H.3
Zaremba, M.4
Tamulaitis, G.5
Siksnys, V.6
Bhagwat, A.S.7
Bochtler, M.8
-
31
-
-
71049141657
-
Structural mechanisms for the 50-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII
-
Golovenko, D., Manakova, E., Tamulaitiene, G., Grazulis, S. and Siksnys, V. (2009) Structural mechanisms for the 50-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res., 37, 6613-6624.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 6613-6624
-
-
Golovenko, D.1
Manakova, E.2
Tamulaitiene, G.3
Grazulis, S.4
Siksnys, V.5
-
32
-
-
0028988416
-
Mg2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 A resolution
-
Kostrewa, D. and Winkler, F.K. (1995) Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution. Biochemistry, 34, 683-696.
-
(1995)
Biochemistry
, vol.34
, pp. 683-696
-
-
Kostrewa, D.1
Winkler, F.K.2
-
33
-
-
0032502924
-
Role of protein-induced bending in the specificity of DNA recognition: Crystal structure of EcoRV endonuclease complexed with d(AAAGAT)+d(ATCTT
-
Horton, N.C. and Perona, J.J. (1998) Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT)+d(ATCTT). J. Mol. Biol., 277, 779-787.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 779-787
-
-
Horton, N.C.1
Perona, J.J.2
-
34
-
-
33644851082
-
DNA nicking by HinP1I endonuclease: Bending, base flipping and minor groove expansion
-
Horton, J.R., Zhang, X., Maunus, R., Yang, Z., Wilson, G.G., Roberts, R.J. and Cheng, X. (2006) DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Nucleic Acids Res., 34, 939-948.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 939-948
-
-
Horton, J.R.1
Zhang, X.2
Maunus, R.3
Yang, Z.4
Wilson, G.G.5
Roberts, R.J.6
Cheng, X.7
-
35
-
-
0017819050
-
A restriction enzyme Tha i from the thermophilic mycoplasma Thermoplasma acidophilum
-
McConnell, D.J., Searcy, D.G. and Sutcliffe, J.G. (1978) A restriction enzyme Tha I from the thermophilic mycoplasma Thermoplasma acidophilum. Nucleic Acids Res., 5, 1729-1739.
-
(1978)
Nucleic Acids Res.
, vol.5
, pp. 1729-1739
-
-
McConnell, D.J.1
Searcy, D.G.2
Sutcliffe, J.G.3
-
36
-
-
0034727087
-
The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum
-
Ruepp, A., Graml, W., Santos-Martinez, M.L., Koretke, K.K., Volker, C., Mewes, H.W., Frishman, D., Stocker, S., Lupas, A.N. and Baumeister, W. (2000) The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature, 407, 508-513.
-
(2000)
Nature
, vol.407
, pp. 508-513
-
-
Ruepp, A.1
Graml, W.2
Santos-Martinez, M.L.3
Koretke, K.K.4
Volker, C.5
Mewes, H.W.6
Frishman, D.7
Stocker, S.8
Lupas, A.N.9
Baumeister, W.10
-
37
-
-
0021761269
-
Methylation of either cytosine in the recognition sequence CGCG inhibits ThaI cleavage of DNA
-
Strobl, J.S. and Thompson, E.B. (1984) Methylation of either cytosine in the recognition sequence CGCG inhibits ThaI cleavage of DNA. Nucleic Acids Res., 12, 8073-8083.
-
(1984)
Nucleic Acids Res.
, vol.12
, pp. 8073-8083
-
-
Strobl, J.S.1
Thompson, E.B.2
-
38
-
-
0030046809
-
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.
-
(1996)
Science
, vol.271
, pp. 778-784
-
-
Werner, M.H.1
Gronenborn, A.M.2
Clore, G.M.3
-
39
-
-
77953174272
-
DIBER: Protein, DNA or both?
-
Chojnowski, G. and Bochtler, M. (2010) DIBER: protein, DNA or both? Acta Crystallogr. D Biol. Crystallogr., 66, 643-653.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 643-653
-
-
Chojnowski, G.1
Bochtler, M.2
-
41
-
-
0028103275
-
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
-
-
-
42
-
-
6344268835
-
Enhancements in AUTOSHARP and SHARP with applications to difficult phasing problems
-
Bricogne, G., Vonrhein, W., Paciorek, C., Flensburg, M., Schiltz, E., Blanc, P., Rovesi, R. and Evans, M.G. (2002) Enhancements in AUTOSHARP and SHARP with applications to difficult phasing problems. Acta Cryst., A58(Suppl.), C239.
-
(2002)
Acta Cryst.
, vol.A58
, Issue.SUPPL.
-
-
Bricogne, G.1
Vonrhein, W.2
Paciorek, C.3
Flensburg, M.4
Schiltz, E.5
Blanc, P.6
Rovesi, R.7
Evans, M.G.8
-
43
-
-
0347383760
-
ARP/wARP and automatic interpretation of protein electron density maps
-
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.
-
(2003)
Methods Enzymol.
, vol.374
, pp. 229-244
-
-
Morris, R.J.1
Perrakis, A.2
Lamzin, V.S.3
-
44
-
-
50349085962
-
3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
-
Lu, X.J. and Olson, W.K. (2008) 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat. Protoc., 3, 1213-1227.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1213-1227
-
-
Lu, X.J.1
Olson, W.K.2
-
45
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W.G. and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr., 66, 486-501.
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
46
-
-
0030924992
-
Refinement of macromolecular structures by the maximum-likelihood method
-
Murshudov, G.N., Vagin, A.A. and Dodson, E.J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr., 53, 240-255.
-
(1997)
Acta Crystallogr. D Biol. Crystallogr.
, vol.53
, pp. 240-255
-
-
Murshudov, G.N.1
Vagin, A.A.2
Dodson, E.J.3
-
47
-
-
37049014272
-
Version 1.2 of the crystallography and NMR system
-
Brunger, A.T. (2007) Version 1.2 of the crystallography and NMR system. Nat. Protoc., 2, 2728-2733.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 2728-2733
-
-
Brunger, A.T.1
-
48
-
-
34047245428
-
A sliding restriction enzyme pauses
-
Pingoud, A. and Wende, W. (2007) A sliding restriction enzyme pauses. Structure, 15, 391-393.
-
(2007)
Structure
, vol.15
, pp. 391-393
-
-
Pingoud, A.1
Wende, W.2
-
49
-
-
0034885432
-
Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement
-
Huai, Q., Colandene, J.D., Topal, M.D. and Ke, H. (2001) Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat. Struct. Biol., 8, 665-669.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 665-669
-
-
Huai, Q.1
Colandene, J.D.2
Topal, M.D.3
Ke, H.4
-
50
-
-
0034660061
-
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. and Ke, H. (2000) Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase. EMBO J., 19, 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
-
51
-
-
77954288774
-
Dali server: Conservation mapping in 3D
-
Holm, L. and Rosenstrom, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res., 38(Suppl.), W545-W549.
-
(2010)
Nucleic Acids Res.
, vol.38
, Issue.SUPPL.
-
-
Holm, L.1
Rosenstrom, P.2
-
52
-
-
0032708112
-
A novel endonuclease mechanism directly visualized for I-PpoI
-
Galburt, E.A., Chevalier, B., Tang, W., Jurica, M.S., Flick, K.E., Monnat, R.J. Jr and Stoddard, B.L. (1999) A novel endonuclease mechanism directly visualized for I-PpoI. Nat. Struct. Biol., 6, 1096-1099.
-
(1999)
Nat. Struct. Biol.
, vol.6
, pp. 1096-1099
-
-
Galburt, E.A.1
Chevalier, B.2
Tang, W.3
Jurica, M.S.4
Flick, K.E.5
Monnat Jr., R.J.6
Stoddard, B.L.7
-
53
-
-
0035906281
-
Identification of a PD-(D/ E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs
-
Bujnicki, J.M. and Rychlewski, L. (2001) Identification of a PD-(D/ E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs. Gene, 267, 183-191.
-
(2001)
Gene
, vol.267
, pp. 183-191
-
-
Bujnicki, J.M.1
Rychlewski, L.2
-
54
-
-
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
-
Skirgaila, R., Grazulis, S., Bozic, D., Huber, R. and Siksnys, V. (1998) 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, 473-481.
-
(1998)
J. Mol. Biol.
, vol.279
, pp. 473-481
-
-
Skirgaila, R.1
Grazulis, S.2
Bozic, D.3
Huber, R.4
Siksnys, V.5
-
55
-
-
0032506110
-
Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases
-
Horton, N.C., Newberry, K.J. and Perona, J.J. (1998) Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. Proc. Natl Acad. Sci. USA, 95, 13489-13494.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 13489-13494
-
-
Horton, N.C.1
Newberry, K.J.2
Perona, J.J.3
-
56
-
-
70349784082
-
Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: A quantum mechanical/molecular mechanical analysis
-
Imhof, P., Fischer, S. and Smith, J.C. (2009) Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis. Biochemistry, 48, 9061-9075.
-
(2009)
Biochemistry
, vol.48
, pp. 9061-9075
-
-
Imhof, P.1
Fischer, S.2
Smith, J.C.3
-
57
-
-
33846165757
-
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism
-
Mones, L., Simon, I. and Fuxreiter, M. (2007) Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism. Biol. Chem., 388, 73-78.
-
(2007)
Biol. Chem.
, vol.388
, pp. 73-78
-
-
Mones, L.1
Simon, I.2
Fuxreiter, M.3
-
58
-
-
0029075461
-
Molecular basis of human 46X, y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex
-
Werner, M.H., Huth, J.R., Gronenborn, A.M. and Clore, G.M. (1995) Molecular basis of human 46X, Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell, 81, 705-714.
-
(1995)
Cell
, vol.81
, pp. 705-714
-
-
Werner, M.H.1
Huth, J.R.2
Gronenborn, A.M.3
Clore, G.M.4
-
59
-
-
0030451819
-
Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
-
Rice, P.A., Yang, S., Mizuuchi, K. and Nash, H.A. (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell, 87, 1295-1306.
-
(1996)
Cell
, vol.87
, pp. 1295-1306
-
-
Rice, P.A.1
Yang, S.2
Mizuuchi, K.3
Nash, H.A.4
-
60
-
-
0041312645
-
Flexible DNA bending in HU-DNA cocrystal structures
-
Swinger, K.K., Lemberg, K.M., Zhang, Y. and Rice, P.A. (2003) Flexible DNA bending in HU-DNA cocrystal structures. EMBO J., 22, 3749-3760.
-
(2003)
EMBO J.
, vol.22
, pp. 3749-3760
-
-
Swinger, K.K.1
Lemberg, K.M.2
Zhang, Y.3
Rice, P.A.4
-
61
-
-
33846954751
-
Shaping the Borrelia burgdorferi genome: Crystal structure and binding properties of the DNA-bending protein Hbb
-
Mouw, K.W. and Rice, P.A. (2007) Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb. Mol. Microbiol., 63, 1319-1330.
-
(2007)
Mol. Microbiol.
, vol.63
, pp. 1319-1330
-
-
Mouw, K.W.1
Rice, P.A.2
-
62
-
-
0028173030
-
Crystal structure of LacI member, PurR, bound to DNA: Minor groove binding by alpha helices
-
Schumacher, M.A., Choi, K.Y., Zalkin, H. and Brennan, R.G. (1994) Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices. Science, 266, 763-770.
-
(1994)
Science
, vol.266
, pp. 763-770
-
-
Schumacher, M.A.1
Choi, K.Y.2
Zalkin, H.3
Brennan, R.G.4
-
63
-
-
0032510217
-
The hyperthermophile chromosomal protein Sac7d sharply kinks DNA
-
Robinson, H., Gao, Y.G., McCrary, B.S., Edmondson, S.P., Shriver, J.W. and Wang, A.H. (1998) The hyperthermophile chromosomal protein Sac7d sharply kinks DNA. Nature, 392, 202-205.
-
(1998)
Nature
, vol.392
, pp. 202-205
-
-
Robinson, H.1
Gao, Y.G.2
McCrary, B.S.3
Edmondson, S.P.4
Shriver, J.W.5
Wang, A.H.6
-
64
-
-
0042161878
-
Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers
-
Remenyi, A., Lins, K., Nissen, L.J., Reinbold, R., Scholer, H.R. and Wilmanns, M. (2003) Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers. Genes Dev., 17, 2048-2059.
-
(2003)
Genes Dev.
, vol.17
, pp. 2048-2059
-
-
Remenyi, A.1
Lins, K.2
Nissen, L.J.3
Reinbold, R.4
Scholer, H.R.5
Wilmanns, M.6
-
65
-
-
64649095458
-
The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms
-
Palasingam, P., Jauch, R., Ng, C.K. and Kolatkar, P.R. (2009) The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms. J. Mol. Biol., 388, 619-630.
-
(2009)
J. Mol. Biol.
, vol.388
, pp. 619-630
-
-
Palasingam, P.1
Jauch, R.2
Ng, C.K.3
Kolatkar, P.R.4
-
66
-
-
0036404246
-
The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding
-
Masse, J.E., Wong, B., Yen, Y.M., Allain, F.H., Johnson, R.C. and Feigon, J. (2002) The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding. J. Mol. Biol., 323, 263-284.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 263-284
-
-
Masse, J.E.1
Wong, B.2
Yen, Y.M.3
Allain, F.H.4
Johnson, R.C.5
Feigon, J.6
-
67
-
-
0027504913
-
Crystal structure of a yeast TBP/TATA-box complex
-
Kim, Y., Geiger, J.H., Hahn, S. and Sigler, P.B. (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520.
-
(1993)
Nature
, vol.365
, pp. 512-520
-
-
Kim, Y.1
Geiger, J.H.2
Hahn, S.3
Sigler, P.B.4
-
68
-
-
0027483012
-
Co-crystal structure of TBP recognizing the minor groove of a TATA element
-
Kim, J.L., Nikolov, D.B. and Burley, S.K. (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
-
(1993)
Nature
, vol.365
, pp. 520-527
-
-
Kim, J.L.1
Nikolov, D.B.2
Burley, S.K.3
-
69
-
-
0028010888
-
HhaI methyltransferase flips its target base out of the DNA helix
-
Klimasauskas, S., Kumar, S., Roberts, R.J. and Cheng, X. (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell, 76, 357-369.
-
(1994)
Cell
, vol.76
, pp. 357-369
-
-
Klimasauskas, S.1
Kumar, S.2
Roberts, R.J.3
Cheng, X.4
-
70
-
-
0033544707
-
Recognition of a TG mismatch: The crystal structure of very short patch repair endonuclease in complex with a DNA duplex
-
Tsutakawa, S.E., Jingami, H. and Morikawa, K. (1999) Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell, 99, 615-623.
-
(1999)
Cell
, vol.99
, pp. 615-623
-
-
Tsutakawa, S.E.1
Jingami, H.2
Morikawa, K.3
-
71
-
-
0034641938
-
Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA
-
Obmolova, G., Ban, C., Hsieh, P. and Yang, W. (2000) Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature, 407, 703-710.
-
(2000)
Nature
, vol.407
, pp. 703-710
-
-
Obmolova, G.1
Ban, C.2
Hsieh, P.3
Yang, W.4
-
72
-
-
0034641947
-
The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch
-
Lamers, M.H., Perrakis, A., Enzlin, J.H., Winterwerp, H.H., de Wind, N. and Sixma, T.K. (2000) The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch. Nature, 407, 711-717.
-
(2000)
Nature
, vol.407
, pp. 711-717
-
-
Lamers, M.H.1
Perrakis, A.2
Enzlin, J.H.3
Winterwerp, H.H.4
De Wind, N.5
Sixma, T.K.6
-
73
-
-
33644511436
-
Structure of a DNA glycosylase searching for lesions
-
Banerjee, A., Santos, W.L. and Verdine, G.L. (2006) Structure of a DNA glycosylase searching for lesions. Science, 311, 1153-1157.
-
(2006)
Science
, vol.311
, pp. 1153-1157
-
-
Banerjee, A.1
Santos, W.L.2
Verdine, G.L.3
-
74
-
-
72049102668
-
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme
-
Qi, Y., Spong, M.C., Nam, K., Banerjee, A., Jiralerspong, S., Karplus, M. and Verdine, G.L. (2009) Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature, 462, 762-766.
-
(2009)
Nature
, vol.462
, pp. 762-766
-
-
Qi, Y.1
Spong, M.C.2
Nam, K.3
Banerjee, A.4
Jiralerspong, S.5
Karplus, M.6
Verdine, G.L.7
-
75
-
-
1342304229
-
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase
-
Fromme, J.C., Banerjee, A., Huang, S.J. and Verdine, G.L. (2004) Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase. Nature, 427, 652-656.
-
(2004)
Nature
, vol.427
, pp. 652-656
-
-
Fromme, J.C.1
Banerjee, A.2
Huang, S.J.3
Verdine, G.L.4
-
76
-
-
0029904839
-
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
-
Slupphaug, G., Mol, C.D., Kavli, B., Arvai, A.S., Krokan, H.E. and Tainer, J.A. (1996) A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature, 384, 87-92.
-
(1996)
Nature
, vol.384
, pp. 87-92
-
-
Slupphaug, G.1
Mol, C.D.2
Kavli, B.3
Arvai, A.S.4
Krokan, H.E.5
Tainer, J.A.6
-
77
-
-
0032498302
-
Crystal structure of a G:T/U mismatch-specific DNA glycosylase: Mismatch recognition by complementary-strand interactions
-
Barrett, T.E., Savva, R., Panayotou, G., Barlow, T., Brown, T., Jiricny, J. and Pearl, L.H. (1998) Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. Cell, 92, 117-129.
-
(1998)
Cell
, vol.92
, pp. 117-129
-
-
Barrett, T.E.1
Savva, R.2
Panayotou, G.3
Barlow, T.4
Brown, T.5
Jiricny, J.6
Pearl, L.H.7
-
78
-
-
42549128712
-
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA
-
Yang, C.G., Yi, C., Duguid, E.M., Sullivan, C.T., Jian, X., Rice, P.A. and He, C. (2008) Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature, 452, 961-965.
-
(2008)
Nature
, vol.452
, pp. 961-965
-
-
Yang, C.G.1
Yi, C.2
Duguid, E.M.3
Sullivan, C.T.4
Jian, X.5
Rice, P.A.6
He, C.7
-
79
-
-
57749198023
-
Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex
-
Scrima, A., Konickova, R., Czyzewski, B.K., Kawasaki, Y., Jeffrey, P.D., Groisman, R., Nakatani, Y., Iwai, S., Pavletich, N.P. and Thoma, N.H. (2008) Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex. Cell, 135, 1213-1223.
-
(2008)
Cell
, vol.135
, pp. 1213-1223
-
-
Scrima, A.1
Konickova, R.2
Czyzewski, B.K.3
Kawasaki, Y.4
Jeffrey, P.D.5
Groisman, R.6
Nakatani, Y.7
Iwai, S.8
Pavletich, N.P.9
Thoma, N.H.10
-
80
-
-
34948892722
-
Recognition of DNA damage by the Rad4 nucleotide excision repair protein
-
Min, J.H. and Pavletich, N.P. (2007) Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature, 449, 570-575.
-
(2007)
Nature
, vol.449
, pp. 570-575
-
-
Min, J.H.1
Pavletich, N.P.2
-
81
-
-
10044280323
-
Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair
-
Mees, A., Klar, T., Gnau, P., Hennecke, U., Eker, A.P., Carell, T. and Essen, L.O. (2004) Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair. Science, 306, 1789-1793.
-
(2004)
Science
, vol.306
, pp. 1789-1793
-
-
Mees, A.1
Klar, T.2
Gnau, P.3
Hennecke, U.4
Eker, A.P.5
Carell, T.6
Essen, L.O.7
|