Pingoud AM: Restriction endonucleases. In Nucleic Acids and Molecular Biology. Volume 14. Edited by: Gross HJ. Berlin, Heidelberg, Springer-Verlag; 2004:442.
Google Scholar
Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SK, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY: A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 2003, 31: 1805–1812. 10.1093/nar/gkg274
Article
PubMed Central
CAS
PubMed
Google Scholar
Roberts RJ, Vincze T, Posfai J, Macelis D: REBASE: restriction enzymes and methyltransferases. Nucleic Acids Res 2003, 31: 418–420. 10.1093/nar/gkg069
Article
PubMed Central
CAS
PubMed
Google Scholar
Taylor JD, Halford SE: Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry 1989, 28: 6198–6207.
Article
CAS
PubMed
Google Scholar
Bujnicki JM: Molecular phylogenetics of restriction endonucleases. Nucleic Acids and Molecular Biology. In Restriction Endonucleases. Volume 14. Edited by: Pingoud A. Edited by: Gross HJ. Berlin, Springer-Verlag; 2004:63–87.
Chapter
Google Scholar
Fuxreiter M, Simon I: Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases. Protein Sci 2002, 11: 1978–1983. 10.1110/ps.4980102
Article
PubMed Central
CAS
PubMed
Google Scholar
Huai Q, Colandene JD, Chen Y, Luo F, Zhao Y, Topal MD, Ke H: Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase. Embo J 2000, 19: 3110–3118. 10.1093/emboj/19.12.3110
Article
PubMed Central
CAS
PubMed
Google Scholar
Bujnicki JM: Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol 2000, 50: 39–44.
CAS
PubMed
Google Scholar
Bujnicki JM: Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. Acta Biochim Pol 2001, 48: 935–967.
CAS
PubMed
Google Scholar
Bujnicki JM, Rychlewski L: 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 2001, 3: 69–72.
CAS
PubMed
Google Scholar
Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A: Evolutionary relationship between different subgroups of restriction endonucleases. J Biol Chem 2002, 277: 14306–14314. 10.1074/jbc.M111625200
Article
CAS
PubMed
Google Scholar
Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Luder G, Xu SY, Pingoud A: PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. J Mol Biol 2003, 329: 913–929. 10.1016/S0022-2836(03)00523-0
Article
CAS
PubMed
Google Scholar
Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Luder G, Morgan R, Kubareva E, Pingoud A: Specificity changes in the evolution of Type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences. J Biol Chem 2004.
Google Scholar
Bujnicki JM: A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide. Acta Microbiol Pol 2001, 50: 219–231.
CAS
PubMed
Google Scholar
Friedhoff P, Lurz R, Luder G, Pingoud A: Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops. J Biol Chem 2001, 276: 23581–23588. 10.1074/jbc.M101694200
Article
CAS
PubMed
Google Scholar
Lagunavicius A, Sasnauskas G, Halford SE, Siksnys V: The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre. J Mol Biol 2003, 326: 1051–1064. 10.1016/S0022-2836(03)00020-2
Article
CAS
PubMed
Google Scholar
Bujnicki JM, 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. 10.1016/S0968-0004(00)01690-X
Article
CAS
PubMed
Google Scholar
Aravind L, Makarova KS, Koonin EV: SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 2000, 28: 3417–3432. 10.1093/nar/28.18.3417
Article
PubMed Central
CAS
PubMed
Google Scholar
Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V: Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucleic Acids Res 2004, 32: 6129–6135. 10.1093/nar/gkh951
Article
PubMed Central
CAS
PubMed
Google Scholar
Qiang BQ, Schildkraut I: A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. Nucleic Acids Res 1984, 12: 4507–4516.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wentzell LM, Nobbs TJ, Halford SE: The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J Mol Biol 1995, 248: 581–595. 10.1006/jmbi.1995.0244
Article
CAS
PubMed
Google Scholar
Nobbs TJ, Szczelkun MD, Wentzell LM, Halford SE: DNA excision by the Sfi I restriction endonuclease. J Mol Biol 1998, 281: 419–432. 10.1006/jmbi.1998.1966
Article
CAS
PubMed
Google Scholar
Wentzell LM, Halford SE: DNA looping by the Sfi I restriction endonuclease. J Mol Biol 1998, 281: 433–444. 10.1006/jmbi.1998.1967
Article
CAS
PubMed
Google Scholar
Watson MA, Gowers DM, Halford SE: Alternative geometries of DNA looping: an analysis using the SfiI endonuclease. J Mol Biol 2000, 298: 461–475. 10.1006/jmbi.2000.3676
Article
CAS
PubMed
Google Scholar
Embleton ML, Vologodskii AV, Halford SE: Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA. J Mol Biol 2004, 339: 53–66. 10.1016/j.jmb.2004.03.046
Article
CAS
PubMed
Google Scholar
Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A: Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000, 29: 291–325. 10.1146/annurev.biophys.29.1.291
Article
CAS
PubMed
Google Scholar
Bujnicki JM: Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. Curr Protein Pept Sci 2003, 4: 327–337.
Article
CAS
PubMed
Google Scholar
Godzik A: Fold recognition methods. Methods Biochem Anal 2003, 44: 525–546.
CAS
PubMed
Google Scholar
Kurowski MA, Bujnicki JM: GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003, 31: 3305–3307. 10.1093/nar/gkg557
Article
PubMed Central
CAS
PubMed
Google Scholar
Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE: Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. Embo J 1998, 17: 5466–5476. 10.1093/emboj/17.18.5466
Article
PubMed Central
CAS
PubMed
Google Scholar
Shi J, Blundell TL, Mizuguchi K: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Mol Biol 2001, 310: 243–257. 10.1006/jmbi.2001.4762
Article
CAS
PubMed
Google Scholar
Fischer D: Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput 2000, 119–130.
Google Scholar
Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R: Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 2003, 53 Suppl 6: 491–496. 10.1002/prot.10540
Article
PubMed
Google Scholar
Kelley LA, MacCallum RM, Sternberg MJ: Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 2000, 299: 499–520. 10.1006/jmbi.2000.3741
Article
CAS
PubMed
Google Scholar
Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS: The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J 1993, 12: 1781–1795.
PubMed Central
CAS
PubMed
Google Scholar
Lundstrom J, Rychlewski L, Bujnicki JM, Elofsson A: Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001, 10: 2354–2362. 10.1110/ps.08501
Article
PubMed Central
CAS
PubMed
Google Scholar
Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM: A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 2003, 53 Suppl 6: 369–379. 10.1002/prot.10545
Article
PubMed
Google Scholar
Bath AJ, Milsom SE, Gormley NA, Halford SE: Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J Biol Chem 2002, 277: 4024–4033. 10.1074/jbc.M108441200
Article
CAS
PubMed
Google Scholar
Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R: Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat Struct Biol 2000, 7: 792–799. 10.1038/79032
Article
CAS
PubMed
Google Scholar
Bozic D, Grazulis S, Siksnys V, Huber R: Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution. J Mol Biol 1996, 255: 176–186. 10.1006/jmbi.1996.0015
Article
CAS
PubMed
Google Scholar
Grazulis S, Deibert M, Rimseliene R, Skirgaila R, Sasnauskas G, Lagunavicius A, Repin V, Urbanke C, Huber R, Siksnys V: Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucleic Acids Res 2002, 30: 876–885. 10.1093/nar/30.4.876
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhou XE, Wang Y, Reuter M, Mucke M, Kruger DH, Meehan EJ, Chen L: Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J Mol Biol 2004, 335: 307–319. 10.1016/j.jmb.2003.10.030
Article
CAS
PubMed
Google Scholar
Mucke M, Grelle G, Behlke J, Kraft R, Kruger DH, Reuter M: EcoRII: a restriction enzyme evolving recombination functions? Embo J 2002, 21: 5262–5268. 10.1093/emboj/cdf514
Article
PubMed Central
PubMed
Google Scholar
Siksnys V, Skirgaila R, Sasnauskas G, Urbanke C, Cherny D, Grazulis S, Huber R: The Cfr10I restriction enzyme is functional as a tetramer. J Mol Biol 1999, 291: 1105–1118. 10.1006/jmbi.1999.2977
Article
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389–3402. 10.1093/nar/25.17.3389
Article
PubMed Central
CAS
PubMed
Google Scholar
McGuffin LJ, Bryson K, Jones DT: The PSIPRED protein structure prediction server. Bioinformatics 2000, 16: 404–405. 10.1093/bioinformatics/16.4.404
Article
CAS
PubMed
Google Scholar
Rost B, Yachdav G, Liu J: The PredictProtein server. Nucleic Acids Res 2004, 32: W321–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ouali M, King RD: Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000, 9: 1162–1176.
Article
PubMed Central
CAS
PubMed
Google Scholar
Adamczak R, Porollo A, Meller J: Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 2004, 56: 753–767. 10.1002/prot.20176
Article
CAS
PubMed
Google Scholar
Cuff JA, Barton GJ: Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000, 40: 502–511. 10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q
Article
CAS
PubMed
Google Scholar
Meiler J, Baker D: Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci U S A 2003, 100: 12105–12110. 10.1073/pnas.1831973100
Article
PubMed Central
CAS
PubMed
Google Scholar
Cuff JA, Clamp ME, Siddiqui AS, Finlay M, Barton GJ: JPred: a consensus secondary structure prediction server. Bioinformatics 1998, 14: 892–893. 10.1093/bioinformatics/14.10.892
Article
CAS
PubMed
Google Scholar
Rychlewski L, Jaroszewski L, Li W, Godzik A: Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000, 9: 232–241.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jones DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999, 287: 797–815. 10.1006/jmbi.1999.2583
Article
CAS
PubMed
Google Scholar
Zhou H, Zhou Y: Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004, 55: 1005–1013. 10.1002/prot.20007
Article
CAS
PubMed
Google Scholar
Fiser A, Sali A: Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003, 374: 461–491.
Article
CAS
PubMed
Google Scholar
Luthy R, Bowie JU, Eisenberg D: Assessment of protein models with three-dimensional profiles. Nature 1992, 356: 83–85. 10.1038/356083a0
Article
CAS
PubMed
Google Scholar
Sasin JM, Bujnicki JM: COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res 2004, 32: W586–9. 10.1093/nar/gkh032
Article
PubMed Central
CAS
PubMed
Google Scholar