Primary Citation PubMed: 9488644
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Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation.
(2005) Nucleic Acids Res 33
PubMed: 16314322 | PubMedCentral: PMC1298917 | DOI: 10.1093/nar/gki935
A covalent model of the DNA–topoisomerase complex was set-up, with the position of the linker domain (missing in the covalent structure, PDB code 1a31) built using the non-covalent structure (... DB code 1a36).
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
Topoisomerase I 1a31 * A Topoisomerase I H. sapiens 2.1 AAAAAGACCCTGAAAAACCCCT 1a35 A Topoisomerase I H. sapiens 2.5 AAAAAGACCCTGAAAAACCCCT 1a36 A Topoisomerase I H. sapiens 2.8 AAAAAGACTTAGAAAAATTTTT... Each entry is provided with the four-digit PDB code, the name, the source, resolution and the aligned sequences of DNA to which the protein is bound in the crystal structure.
Publication Year: 2000
Insights into protein-DNA interactions through structure network analysis.
(2008) PLoS Comput Biol 4
PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170
Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).
Publication Year: 2008
Evaluation of two models for human topoisomerase I interaction with dsDNA and camptothecin derivatives.
(2011) PLoS One 6
PubMed: 21912628 | PubMedCentral: PMC3166174 | DOI: 10.1371/journal.pone.0024314
pdb scissile strand base 11 is a guanine), and the base pairing non-scissile strand adenine in the 1A31.
pdb structure were deleted leaving the corresponding DNA from the 1A31.
Publication Year: 2011
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
Sequence selectivity of the cleavage sites induced by topoisomerase I inhibitors: a molecular dynamics study.
(2013) Nucleic Acids Res 41
PubMed: 24021629 | PubMedCentral: PMC3905861 | DOI: 10.1093/nar/gkt791
This loop is known to have a direct impact on the flexibility of the linker domain ( 24 ), as the loop and the linker domain are also absent in the X-ray crystallographic structure of the Top1-DNA bin... ry complex (PDB: 1A31), but observable in the drug-bound ternary complexes (PDB: 1K4T) ( Supplementary Figure S3 ) ( 50 ).
Publication Year: 2013
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