-
1
-
-
0025284372
-
Restriction enzymes and their isoschizomers
-
Roberts, R. J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18, 2331-2365 (1990)
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 2331-2365
-
-
Roberts, R.J.1
-
2
-
-
0035883519
-
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
-
Kobayashi, I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res. 29, 3742-3756 (2001)
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 3742-3756
-
-
Kobayashi, I.1
-
3
-
-
0028901038
-
Selfish behavior of restrictionmodification systems
-
Naito, T., Kusano, K. & Kobayashi, I. Selfish behavior of restrictionmodification systems. Science 267, 897-899 (1995)
-
(1995)
Science
, vol.267
, pp. 897-899
-
-
Naito, T.1
Kusano, K.2
Kobayashi, I.3
-
4
-
-
0141954129
-
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, 327-337 (2003)
-
(2003)
Curr. Protein Pept. Sci
, vol.4
, pp. 327-337
-
-
Bujnicki J., .M.1
-
5
-
-
17044403057
-
Type II restriction endonucleases: Structure and mechanism
-
Pingoud, A., Fuxreiter, M., Pingoud, V. & Wende, W. Type II restriction endonucleases: structure and mechanism. Cell Mol. Life Sci. 62, 685-707 (2005)
-
(2005)
Cell Mol. Life Sci
, vol.62
, pp. 685-707
-
-
Pingoud, A.1
Fuxreiter, M.2
Pingoud, V.3
Wende, W.4
-
6
-
-
46349101158
-
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
-
Orlowski, J. & Bujnicki, J. Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res. 36, 3552-3569 (2008)
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3552-3569
-
-
Orlowski, J.1
Bujnicki, J.2
-
7
-
-
27644485012
-
Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease
-
Grazulis, S. et al. Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease. Proc. Natl Acad. Sci. USA 102, 15797-15802 (2005)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15797-15802
-
-
Grazulis, S.1
-
8
-
-
11344267268
-
Type ii restriction endonuclease rkpni is a member of the hnh nuclease superfamily
-
Saravanan, M., Bujnicki, J. M., Cymerman, I. A., Rao, D. N. & Nagaraja, V. Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucleic Acids Res. 32, 6129-6135 (2004)
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 6129-6135
-
-
Saravanan, M.1
Bujnicki, J.M.2
Cymerman, I.A.3
Rao, D.N.4
Nagaraja, V.5
-
9
-
-
79952332536
-
Hpy188i-dna pre- and postcleavage complexes-snapshots of the giy-yig nuclease mediated catalysis
-
Sokolowska, M., Czapinska, H. & Bochtler, M. Hpy188I-DNA pre- and postcleavage complexes-snapshots of the GIY-YIG nuclease mediated catalysis. Nucleic Acids Res. 39, 1554-1564 (2011)
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 1554-1564
-
-
Sokolowska, M.1
Czapinska, H.2
Bochtler, M.3
-
10
-
-
70349229163
-
On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family
-
Pingoud, V. et al. On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J. Mol. Biol. 393, 140-160 (2009)
-
(2009)
J. Mol. Biol
, vol.393
, pp. 140-160
-
-
Pingoud, V.1
-
11
-
-
27144543021
-
Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (50-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi
-
Ishikawa, K. et al. Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (50-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Res. 33, e112 (2005)
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Ishikawa, K.1
-
12
-
-
34247886142
-
Novel protein fold discovered in the PabI family of restriction enzymes
-
Miyazono, K. et al. Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res. 35, 1908-1918 (2007)
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 1908-1918
-
-
Miyazono, K.1
-
13
-
-
57149101710
-
The helicobacter pylori hpyaxii restrictionmodification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components
-
Humbert, O. & Salama, N. R. The Helicobacter pylori HpyAXII restrictionmodification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components. Nucleic Acids Res. 36, 6893-6906 (2008)
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 6893-6906
-
-
Humbert, O.1
Salama, N.R.2
-
14
-
-
4143149415
-
Site-specific DNA damage recognition by enzyme-induced base flipping
-
Stivers, J. T. Site-specific DNA damage recognition by enzyme-induced base flipping. Prog. Nucleic Acid Res. Mol. Biol. 77, 37-65 (2004)
-
(2004)
Prog. Nucleic Acid Res. Mol. Biol
, vol.77
, pp. 37-65
-
-
Stivers, J.T.1
-
15
-
-
38849207616
-
Extrahelical damaged base recognition by DNA glycosylase enzymes
-
Stivers, J. T. Extrahelical damaged base recognition by DNA glycosylase enzymes. Chemistry 14, 786-793 (2008)
-
(2008)
Chemistry
, vol.14
, pp. 786-793
-
-
Stivers, J.T.1
-
16
-
-
84870683808
-
Recent advances in the structural mechanisms of DNA glycosylases
-
Brooks, S. C., Adhikary, S., Rubinson, E. H. & Eichman, B. F. Recent advances in the structural mechanisms of DNA glycosylases. Biochim. Biophys. Acta 1834, 247-271 (2013)
-
(2013)
Biochim. Biophys. Acta
, vol.1834
, pp. 247-271
-
-
Brooks, S.C.1
Adhikary, S.2
Rubinson, E.H.3
Eichman, B.F.4
-
17
-
-
0034708226
-
Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
-
Bruner, S. D., Norman, D. P. & Verdine, G. L. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA. Nature 403, 859-866 (2000)
-
(2000)
Nature
, vol.403
, pp. 859-866
-
-
Bruner, S.D.1
Norman, D.P.2
Verdine, G.L.3
-
18
-
-
15844379169
-
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA
-
Banerjee, A., Yang, W., Karplus, M. & Verdine, G. L. Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature 434, 612-618 (2005)
-
(2005)
Nature
, vol.434
, pp. 612-618
-
-
Banerjee, A.1
Yang, W.2
Karplus, M.3
Verdine, G.L.4
-
19
-
-
84862489528
-
Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1
-
Crenshaw, C. M. et al. Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. J. Biol. Chem. 287, 24916-24928 (2012)
-
(2012)
J. Biol. Chem
, vol.287
, pp. 24916-24928
-
-
Crenshaw, C.M.1
-
20
-
-
0346435086
-
Dna lesion recognition by the bacterial repair enzyme mutm
-
Fromme, J. C. & Verdine, G. L. DNA lesion recognition by the bacterial repair enzyme MutM. J. Biol. Chem. 278, 51543-51548 (2003)
-
(2003)
J. Biol. Chem
, vol.278
, pp. 51543-51548
-
-
Fromme, J.C.1
Verdine, G.L.2
-
21
-
-
0036294464
-
Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM
-
Fromme, J. C. & Verdine, G. L. Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM. Nat. Struct. Biol. 9, 544-552 (2002)
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 544-552
-
-
Fromme, J.C.1
Verdine, G.L.2
-
22
-
-
0033529716
-
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: Double-nucleotide flipping at abasic sites and three-metal-ion catalysis
-
Hosfield, D. J., Guan, Y., Haas, B. J., Cunningham, R. P. & Tainer, J. A. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98, 397-408 (1999)
-
(1999)
Cell
, vol.98
, pp. 397-408
-
-
Hosfield, D.J.1
Guan, Y.2
Haas, B.J.3
Cunningham, R.P.4
Tainer, J.A.5
-
23
-
-
33646813662
-
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease
-
Bochtler, M. et al. Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease. EMBO J. 25, 2219-2229 (2006)
-
(2006)
EMBO J
, vol.25
, pp. 2219-2229
-
-
Bochtler, M.1
-
24
-
-
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. & Siksnys, V. Structural mechanisms for the 50-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res. 37, 6613-6624 (2009)
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 6613-6624
-
-
Golovenko, D.1
Manakova, E.2
Tamulaitiene, G.3
Grazulis, S.4
Siksnys, V.5
-
25
-
-
56049121435
-
Central base pair flipping and discrimination by PspGI
-
Szczepanowski, R. H. et al. Central base pair flipping and discrimination by PspGI. Nucleic Acids Res. 36, 6109-6117 (2008)
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 6109-6117
-
-
Szczepanowski, R.H.1
-
26
-
-
42649085059
-
Transition-state analysis of the dna repair enzyme muty
-
McCann, J. A. & Berti, P. J. Transition-state analysis of the DNA repair enzyme MutY. J. Am. Chem. Soc. 130, 5789-5797 (2008)
-
(2008)
J. Am. Chem. Soc
, vol.130
, pp. 5789-5797
-
-
McCann, J.A.1
Berti, P.J.2
-
27
-
-
0034700259
-
Kinetic isotope effect studies of the reaction catalysed by uracil DNA glycosylase: Evidence for an oxocarbenium ion-uracil anion intermediate
-
Werner, R. M. & Stivers, J. T. Kinetic isotope effect studies of the reaction catalysed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate. Biochemistry 39, 14054-14064 (2000)
-
(2000)
Biochemistry
, vol.39
, pp. 14054-14064
-
-
Werner, R.M.1
Stivers, J.T.2
-
28
-
-
0035909316
-
Uracil-dna glycosylase acts by substrate autocatalysis
-
Dinner, A. R., Blackburn, G. M. & Karplus, M. Uracil-DNA glycosylase acts by substrate autocatalysis. Nature 413, 752-755 (2001)
-
(2001)
Nature
, vol.413
, pp. 752-755
-
-
Dinner, A.R.1
Blackburn, G.M.2
Karplus, M.3
-
29
-
-
0024462459
-
-
Bailly, V., Verly, W. G., O?Connor, T. & Laval, J. Mechanism of DNA strand nicking at apurinic/apyrimidinic sites by Escherichia coli [formamidopyrimidine]DNA glycosylase. Biochem. J. 262, 581-589 (1989)
-
(1989)
Mechanism of dna strand nicking at apurinic/apyrimidinic sites by Escherichia coli [formamidopyrimidine]DNA glycosylase. Biochem. J
, vol.262
, pp. 581-589
-
-
Bailly, V.1
Verly, W.G.2
Oconnor, T.3
Laval, J.4
-
30
-
-
0028604549
-
Unified catalytic mechanism for DNA glycosylases
-
Dodson, M. L., Michaels, M. L. & Lloyd, R. S. Unified catalytic mechanism for DNA glycosylases. J. Biol. Chem. 269, 32709-32712 (1994)
-
(1994)
J. Biol. Chem
, vol.269
, pp. 32709-32712
-
-
Dodson, M.L.1
Michaels, M.L.2
Lloyd, R.S.3
-
31
-
-
0023657112
-
Mechanism of action of Escherichia coli endonuclease III
-
Kow, Y. W. & Wallace, S. S. Mechanism of action of Escherichia coli endonuclease III. Biochemistry 26, 8200-8206 (1987)
-
(1987)
Biochemistry
, vol.26
, pp. 8200-8206
-
-
Kow, Y.W.1
Wallace, S.S.2
-
32
-
-
0034610336
-
Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG
-
Lau, A. Y., Wyatt, M. D., Glassner, B. J., Samson, L. D. & Ellenberger, T. Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG. Proc. Natl Acad. Sci. USA 97, 13573-13578 (2000)
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 13573-13578
-
-
Lau, A.Y.1
Wyatt, M.D.2
Glassner, B.J.3
Samson, L.D.4
Ellenberger, T.5
-
33
-
-
73249131232
-
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase
-
Lee, S. & Verdine, G. L. Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase. Proc. Natl Acad. Sci. USA 106, 18497-18502 (2009)
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 18497-18502
-
-
Lee, S.1
Verdine, G.L.2
-
34
-
-
0034607641
-
Characteristics of Helicobacter pylori natural transformation
-
Israel, D. A., Lou, A. S. & Blaser, M. J. Characteristics of Helicobacter pylori natural transformation. FEMS Microbiol. Lett. 186, 275-280 (2000)
-
(2000)
FEMS Microbiol. Lett
, vol.186
, pp. 275-280
-
-
Israel, D.A.1
Lou, A.S.2
Blaser, M.J.3
-
36
-
-
79953737180
-
Overview of the CCP4 suite and current developments
-
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D. Biol. Crystallogr. 67, 235-242 (2011)
-
(2011)
Acta Crystallogr D. Biol. Crystallogr.
, vol.67
, pp. 235-242
-
-
Winn, M.D.1
-
37
-
-
0000560808
-
Molrep: An automated program for molecular replacement
-
Vagin, A. & Teplyakov, A. MOLREP: an Automated Program for Molecular Replacement. J. Appl. Cryst. 30, 1022-1025 (1997)
-
(1997)
J. Appl. Cryst
, vol.30
, pp. 1022-1025
-
-
Vagin, A.1
Teplyakov, A.2
-
38
-
-
76449098262
-
Phenix: A comprehensive python-based system for macromolecular structure solution
-
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213-221 (2010)
-
(2010)
Acta Crystallogr D. Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
-
39
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486-501 (2010)
-
(2010)
Acta Crystallogr D. Biol. Crystallogr.
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
40
-
-
74549178560
-
Molprobity: All-atom structure validation for macromolecular crystallography
-
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D. Biol. Crystallogr. 66, 12-21 (2010)
-
(2010)
Acta Crystallogr D. Biol. Crystallogr.
, vol.66
, pp. 12-21
-
-
Chen, V.B.1
-
42
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774-797 (2007)
-
(2007)
J. Mol. Biol
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
|