Primary Citation PubMed: 7819264
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Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
(2005) Nucleic Acids Res 33
PubMed: 15805123 | PubMedCentral: PMC1074309 | DOI: 10.1093/nar/gki337
USA 2003 100 6410 6415 12750473 42 Ban C. Yang W. Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases EMBO J. 1998 17 1526 1534 9482749... Figures and Tables Figure 1 Dimeric form of endonucleases: ( A ) EcoRI–DNA complex (PDB 1CKQ), ( B ) EcoRV–DNA complex (PDB 1RVA), ( C ) BglI–DNA complex (PDB 1DMU).
Publication Year: 2005
An overview of the structures of protein-DNA complexes.
(2000) Genome Biol 1
PubMed: 11104519 | PubMedCentral: PMC138832 | DOI: 10.1186/gb-2000-1-1-reviews001
Endonuclease EcoRV family 1rva * A,B Endonuclease EcoRV E. coli 2.0 ------AAAGATATCTTAAA---GATATCTT- 1rvb A,B Endonuclease EcoRV E. coli 2.1 ------AAAGATATCTTAAA---GATATCTT- 1rvc A,B Endonuclease EcoR... E. coli 2.1 ------AAAGATATCTTAAA---GATATCTT- 2rve A,B Endonuclease EcoRV E. coli 3.0 CGAGCTCGCGAGCTCGCGAGCTCGCGAGCTCG 4rve † A,B,C,G Endonuclease EcoRV E. coli 3.0 -------GGGATATCCCGG----GATATCCC- 1rve A,B Endonuclease EcoRV E. coli 2.5 ------AAAGATATCTTAAA----GATATCTT- 1rv5 A,B Endonuclease EcoRV E. coli 2.1 ------CGGGATATCCC CGG---GATATCCC- 1bgb A,B Endonuclease EcoRV E. coli 2.0 ------AAAGATATCTTAAA---GATATCTT- 1bss A,B Endonuclease EcoRV E. coli 2.0 ------AAAGATATCTTAAA---GATATCTT- 1bua A,B Endonuclease EcoRV E. coli 2.15 ------AAAGACATCTT--------------- 1bsu A,B Endonuclease EcoRV E. coli 2.0 ------AAAGACATCTT--------------- ** **** * 42.
Publication Year: 2000
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
(2010) Nucleic Acids Res 38
PubMed: 20466807 | PubMedCentral: PMC2943626 | DOI: 10.1093/nar/gkq222
These, for instance, involve enzymes that perform their catalytic function on single nucleotides that are flipped out of the helix into a catalytic pocket of the protein (1emh, 7mht), restriction enzy... es clamping themselves around the DNA (3bam,1rva) or proteins with complex dimerization interfaces (1tro, 1f4k).
Publication Year: 2010
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.
(2012) BMC Bioinformatics 13
PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165
Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH ... 000a0; Cro & repressor 1LMB Homeodomain 1FJL, 1HDD, 6PAX LacI repressor 1WET Endonuclease Fok1 1FOK Gamma Delta resolvase 1GDT Hin recombinase 1HCR RAP1 family 1IGN Prd paired domain 1PDN Tc3 transposase 1TC3 Trp repressor 1TRR Diptheria tox repressor 1DDN Transcription factor IIB 1D3U Interferon regulatory 2IRF Catabolite gene activator protein 1RUO Transcription factor 1CF7, 3HTS Ets domain 1BC8 Zinc Co-ordinating β-β-α zinc finger 1ZAA Harmone Nuclear Receptor 2NLL Loop sheet helix 1TSR GAL4 type 1ZME Zipper type Leucine Zipper 1YSA Helix loop helix 1AN2 Other-α Helix Pappilomavirus 1 E2 2BOP Histone 1AOI EBNA1 nuclear protein 1B3T Skn-1 transcription factor 1SKN Cre Recombinase 1CRX High Mobility Group 1QRV MADS box 1MNM β-Sheet TATA box binding 1YTB β-Hairpin/Ribbon MetJ repressor 1CMA Tus replication terminator 1ECR Integration host factor 1IHF Transcription Factor T-domain 1XBR Hyperthermophile DNA 1AZP Arc repressor 1PAR Other ReI homology 1SVC Stat protein 1BF5 Enzyme Methyltransferase 6MHT Endonuclease PvuII 3PVI Endonuclease ecorV 1RVA Endonuclease ecorI 1QPS Endonuclease BamHI 3BAM Enonuclease V 1VAS Dnase I 2DNJ DNA mismatch endonuclease 1CW0 DNA polymerase β 1BPY DNA Polymerase I 2BDP DNA Polymerase T7 1T7P,1CLQ HIV Reverse Transcriptase 2HMI Uracil DNA glycosylase 1SSP 3-Methyladenine DNA glycosylase 1BNK Homing endonuclease 1A73, 1BP7 TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).
Publication Year: 2012
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