-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
77950019411
-
Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme
-
Andersson C.E., Lagerback P., Carlson K. Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme. J. Mol. Biol. 2010, 397:1003-1016.
-
(2010)
J. Mol. Biol.
, vol.397
, pp. 1003-1016
-
-
Andersson, C.E.1
Lagerback, P.2
Carlson, K.3
-
3
-
-
0033105094
-
Conserved domains in DNA repair proteins and evolution of repair systems
-
Aravind L., Walker D.R., Koonin E.V. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 1999, 27:1223-1242.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 1223-1242
-
-
Aravind, L.1
Walker, D.R.2
Koonin, E.V.3
-
4
-
-
0034889360
-
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system
-
Aravind L., Koonin E.V. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res. 2001, 11:1365-1374.
-
(2001)
Genome Res.
, vol.11
, pp. 1365-1374
-
-
Aravind, L.1
Koonin, E.V.2
-
5
-
-
0036468146
-
Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns
-
Belle A., Landthaler M., Shub D.A. Intronless homing: site-specific endonuclease SegF of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns. Genes Dev. 2002, 16:351-362.
-
(2002)
Genes Dev.
, vol.16
, pp. 351-362
-
-
Belle, A.1
Landthaler, M.2
Shub, D.A.3
-
6
-
-
0035150384
-
Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed
-
Bujnicki J.M., Radlinska M., Rychlewski L. Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem. Sci. 2001, 26:9-11.
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 9-11
-
-
Bujnicki, J.M.1
Radlinska, M.2
Rychlewski, L.3
-
7
-
-
0020503897
-
In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments
-
Carlson K., Wiberg J.S. In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments. J. Virol. 1983, 48:18-30.
-
(1983)
J. Virol.
, vol.48
, pp. 18-30
-
-
Carlson, K.1
Wiberg, J.S.2
-
8
-
-
0347990576
-
Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast
-
Coulon S., Gaillard P.H., Chahwan C., McDonald W.H., Yates J.R., Russell P. Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol. Biol. Cell 2004, 15:71-80.
-
(2004)
Mol. Biol. Cell
, vol.15
, pp. 71-80
-
-
Coulon, S.1
Gaillard, P.H.2
Chahwan, C.3
McDonald, W.H.4
Yates, J.R.5
Russell, P.6
-
10
-
-
34250858251
-
Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism
-
Eastberg J.H., Eklund J., Monnat R., Stoddard B.L. Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism. Biochemistry 2007, 46:7215-7225.
-
(2007)
Biochemistry
, vol.46
, pp. 7215-7225
-
-
Eastberg, J.H.1
Eklund, J.2
Monnat, R.3
Stoddard, B.L.4
-
12
-
-
0033588313
-
NMR structure of the N-terminal domain of Saccharomyces cerevisiae RNase HI reveals a fold with a strong resemblance to the N-terminal domain of ribosomal protein L9
-
Evans S.P., Bycroft M. NMR structure of the N-terminal domain of Saccharomyces cerevisiae RNase HI reveals a fold with a strong resemblance to the N-terminal domain of ribosomal protein L9. J. Mol. Biol. 1999, 291:661-669.
-
(1999)
J. Mol. Biol.
, vol.291
, pp. 661-669
-
-
Evans, S.P.1
Bycroft, M.2
-
13
-
-
39449106934
-
Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family
-
Gasiunas G., Sasnauskas G., Tamulaitis G., Urbanke C., Razaniene D., Siksnys V. Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family. Nucleic Acids Res. 2008, 36:938-949.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 938-949
-
-
Gasiunas, G.1
Sasnauskas, G.2
Tamulaitis, G.3
Urbanke, C.4
Razaniene, D.5
Siksnys, V.6
-
14
-
-
3042785825
-
One recognition sequence, seven restriction enzymes, five reaction mechanisms
-
Gowers D.M., Bellamy S.R., Halford S.E. One recognition sequence, seven restriction enzymes, five reaction mechanisms. Nucleic Acids Res. 2004, 32:3469-3479.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 3469-3479
-
-
Gowers, D.M.1
Bellamy, S.R.2
Halford, S.E.3
-
15
-
-
0030596154
-
Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy
-
Hoffman D.W., Cameron C.S., Davies C., White S.W., Ramakrishnan V. Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy. J. Mol. Biol. 1996, 264:1058-1071.
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 1058-1071
-
-
Hoffman, D.W.1
Cameron, C.S.2
Davies, C.3
White, S.W.4
Ramakrishnan, V.5
-
16
-
-
34548267639
-
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
-
Ibryashkina E.M., Zakharova M.V., Baskunov V.B., Bogdanova E.S., Nagornykh M.O., Den'mukhamedov M.M., Melnik B.S., Kolinski A., Gront D., Feder M., et al. Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. BMC Struct. Biol. 2007, 7:48.
-
(2007)
BMC Struct. Biol.
, vol.7
, pp. 48
-
-
Ibryashkina, E.M.1
Zakharova, M.V.2
Baskunov, V.B.3
Bogdanova, E.S.4
Nagornykh, M.O.5
Den'mukhamedov, M.M.6
Melnik, B.S.7
Kolinski, A.8
Gront, D.9
Feder, M.10
-
17
-
-
61349107249
-
Oligomeric structure diversity within the GIY-YIG nuclease family
-
Ibryashkina E.M., Sasnauskas G., Solonin A.S., Zakharova M.V., Siksnys V. Oligomeric structure diversity within the GIY-YIG nuclease family. J. Mol. Biol. 2009, 387:10-16.
-
(2009)
J. Mol. Biol.
, vol.387
, pp. 10-16
-
-
Ibryashkina, E.M.1
Sasnauskas, G.2
Solonin, A.S.3
Zakharova, M.V.4
Siksnys, V.5
-
18
-
-
33846531362
-
Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad
-
Karakas E., Truglio J.J., Croteau D., Rhau B., Wang L., Van Houten B., Kisker C. Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad. EMBO J. 2007, 26:613-622.
-
(2007)
EMBO J.
, vol.26
, pp. 613-622
-
-
Karakas, E.1
Truglio, J.J.2
Croteau, D.3
Rhau, B.4
Wang, L.5
Van Houten, B.6
Kisker, C.7
-
19
-
-
25444522883
-
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
-
Kosinski J., Feder M., Bujnicki J.M. The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function. BMC Bioinformatics 2005, 6:172.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 172
-
-
Kosinski, J.1
Feder, M.2
Bujnicki, J.M.3
-
20
-
-
0033562780
-
Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings
-
Kowalski J.C., Belfort M., Stapleton M.A., Holpert M., Dansereau J.T., Pietrokovski S., Baxter S.M., Derbyshire V. Configuration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings. Nucleic Acids Res. 1999, 27:2115-2125.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2115-2125
-
-
Kowalski, J.C.1
Belfort, M.2
Stapleton, M.A.3
Holpert, M.4
Dansereau, J.T.5
Pietrokovski, S.6
Baxter, S.M.7
Derbyshire, V.8
-
21
-
-
34548232365
-
Inference of macromolecular assemblies from crystalline state
-
Krissinel E., Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 2007, 372:774-797.
-
(2007)
J. Mol. Biol.
, vol.372
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
22
-
-
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., Stoddard B.L. Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding. Structure 2008, 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
-
23
-
-
34447508216
-
Phaser crystallographic software
-
McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J. Appl. Crystallogr. 2007, 40:658-674.
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
24
-
-
0347994100
-
HNH family subclassification leads to identification of commonality in the His-Me endonuclease superfamily
-
Mehta P., Katta K., Krishnaswamy S. HNH family subclassification leads to identification of commonality in the His-Me endonuclease superfamily. Protein Sci. 2004, 13:295-300.
-
(2004)
Protein Sci.
, vol.13
, pp. 295-300
-
-
Mehta, P.1
Katta, K.2
Krishnaswamy, S.3
-
25
-
-
0037022344
-
Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair
-
Moolenaar G.F., van Rossum-Fikkert S., van Kesteren M., Goosen N. Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair. Proc. Natl. Acad. Sci. USA 2002, 99:1467-1472.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 1467-1472
-
-
Moolenaar, G.F.1
van Rossum-Fikkert, S.2
van Kesteren, M.3
Goosen, N.4
-
26
-
-
0038686711
-
Construction of an overproducing strain, purification, and biochemical characterization of the 6His-Eco29kI restriction endonuclease
-
Nikitin D., Mokrishcheva M., Denjmukhametov M., Pertzev A., Zakharova M., Solonin A. Construction of an overproducing strain, purification, and biochemical characterization of the 6His-Eco29kI restriction endonuclease. Protein Expr. Purif. 2003, 30:26-31.
-
(2003)
Protein Expr. Purif.
, vol.30
, pp. 26-31
-
-
Nikitin, D.1
Mokrishcheva, M.2
Denjmukhametov, M.3
Pertzev, A.4
Zakharova, M.5
Solonin, A.6
-
27
-
-
46349101158
-
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
-
Orlowski J., Bujnicki J.M. Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res. 2008, 36:1-13.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 1-13
-
-
Orlowski, J.1
Bujnicki, J.M.2
-
28
-
-
0026518949
-
Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli
-
Pertzev A.V., Ruban N.M., Zakharova M.V., Beletzkaja I.V., Petrov S.I., Kravetz A.N., Solonin A.S. Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli. Nucleic Acids Res. 1992, 20:1991.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 1991
-
-
Pertzev, A.V.1
Ruban, N.M.2
Zakharova, M.V.3
Beletzkaja, I.V.4
Petrov, S.I.5
Kravetz, A.N.6
Solonin, A.S.7
-
29
-
-
6944240085
-
Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements
-
Pyatkov K.I., Arkhipova I.R., Malkova N.V., Finnegan D.J., Evgen'ev M.B. Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements. Proc. Natl. Acad. Sci. USA 2004, 101:14719-14724.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 14719-14724
-
-
Pyatkov, K.I.1
Arkhipova, I.R.2
Malkova, N.V.3
Finnegan, D.J.4
Evgen'ev, M.B.5
-
30
-
-
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., Stoddard B.L. Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI. Structure 2010, 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
-
31
-
-
77957772125
-
-
Solution NMR structure of the protein EF2693 from E. faecalis: Northeast Structural Genomics Consortium target EFR36.
-
Swapna, G.V.T., Bhattacharya, A., Aramini, J.M., Acton, T.B., Ma, L., Xiao, R., Shastry, R., Shih, L., Cunningham, K.E., Montelione, G.T. (2005). Solution NMR structure of the protein EF2693 from E. faecalis: Northeast Structural Genomics Consortium target EFR36. (; ). http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZG2.
-
(2005)
-
-
Swapna, G.V.T.1
Bhattacharya, A.2
Aramini, J.M.3
Acton, T.B.4
Ma, L.5
Xiao, R.6
Shastry, R.7
Shih, L.8
Cunningham, K.E.9
Montelione, G.T.10
-
32
-
-
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., Kisker C. Structural insights into the first incision reaction during nucleotide excision repair. EMBO J. 2005, 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
-
33
-
-
0037022654
-
A cut above: discovery of an alternative excision repair pathway in bacteria
-
Van Houten B., Eisen J.A., Hanawalt P.C. A cut above: discovery of an alternative excision repair pathway in bacteria. Proc. Natl. Acad. Sci. USA 2002, 99:2581-2583.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 2581-2583
-
-
Van Houten, B.1
Eisen, J.A.2
Hanawalt, P.C.3
-
34
-
-
0036828959
-
Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI
-
Van Roey P., Meehan L., Kowalski J.C., Belfort M., Derbyshire V. Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Nat. Struct. Biol. 2002, 9:806-811.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 806-811
-
-
Van Roey, P.1
Meehan, L.2
Kowalski, J.C.3
Belfort, M.4
Derbyshire, V.5
-
35
-
-
0034681350
-
Catalytic sites for 3' and 5' incision of Escherichia coli nucleotide excision repair are both located in UvrC
-
Verhoeven E.E., van Kesteren M., Moolenaar G.F., Visse R., Goosen N. Catalytic sites for 3' and 5' incision of Escherichia coli nucleotide excision repair are both located in UvrC. J. Biol. Chem. 2000, 275:5120-5123.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 5120-5123
-
-
Verhoeven, E.E.1
van Kesteren, M.2
Moolenaar, G.F.3
Visse, R.4
Goosen, N.5
-
36
-
-
0013461295
-
Macromolecular TLS refinement in REFMAC at moderate resolutions
-
Winn M.D., Murshudov G.N., Papiz M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 2003, 374:300-321.
-
(2003)
Methods Enzymol.
, vol.374
, pp. 300-321
-
-
Winn, M.D.1
Murshudov, G.N.2
Papiz, M.Z.3
-
37
-
-
33645962475
-
Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity
-
Yang W., Lee J.Y., Nowotny M. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol. Cell 2006, 22:5-13.
-
(2006)
Mol. Cell
, vol.22
, pp. 5-13
-
-
Yang, W.1
Lee, J.Y.2
Nowotny, M.3
-
38
-
-
0032570833
-
Cloning and sequence analysis of the plasmid-borne genes encoding the Eco29kI restriction and modification enzymes
-
Zakharova M.V., Beletskaya I.V., Kravetz A.N., Pertzev A.V., Mayorov S.G., Shlyapnikov M.G., Solonin A.S. Cloning and sequence analysis of the plasmid-borne genes encoding the Eco29kI restriction and modification enzymes. Gene 1998, 208:177-182.
-
(1998)
Gene
, vol.208
, pp. 177-182
-
-
Zakharova, M.V.1
Beletskaya, I.V.2
Kravetz, A.N.3
Pertzev, A.V.4
Mayorov, S.G.5
Shlyapnikov, M.G.6
Solonin, A.S.7
-
39
-
-
17644392830
-
TM-align: a protein structure alignment algorithm based on the TM-score
-
Zhang Y., Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005, 33:2302-2309.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
|