ID TOP3_VIBCH Reviewed; 647 AA. AC Q9KQF5; DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-2000, sequence version 1. DT 27-MAR-2024, entry version 131. DE RecName: Full=DNA topoisomerase 3 {ECO:0000255|HAMAP-Rule:MF_00953}; DE EC=5.6.2.1 {ECO:0000255|HAMAP-Rule:MF_00953}; DE AltName: Full=DNA topoisomerase III {ECO:0000255|HAMAP-Rule:MF_00953}; GN Name=topB {ECO:0000255|HAMAP-Rule:MF_00953}; GN OrderedLocusNames=VC_2043; OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961). OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae; OC Vibrio. OX NCBI_TaxID=243277; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 39315 / El Tor Inaba N16961; RX PubMed=10952301; DOI=10.1038/35020000; RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L., RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R., RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D., RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A., RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L., RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.; RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio RT cholerae."; RL Nature 406:477-483(2000). CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA, which CC is introduced during the DNA replication and transcription, by CC transiently cleaving and rejoining one strand of the DNA duplex. CC Introduces a single-strand break via transesterification at a target CC site in duplex DNA. The scissile phosphodiester is attacked by the CC catalytic tyrosine of the enzyme, resulting in the formation of a DNA- CC (5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH CC DNA strand. The free DNA strand then undergoes passage around the CC unbroken strand, thus removing DNA supercoils. Finally, in the CC religation step, the DNA 3'-OH attacks the covalent intermediate to CC expel the active-site tyrosine and restore the DNA phosphodiester CC backbone. {ECO:0000255|HAMAP-Rule:MF_00953}. CC -!- CATALYTIC ACTIVITY: CC Reaction=ATP-independent breakage of single-stranded DNA, followed by CC passage and rejoining.; EC=5.6.2.1; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00953}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00953}; CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_00953}; CC -!- SIMILARITY: Belongs to the type IA topoisomerase family. CC {ECO:0000255|HAMAP-Rule:MF_00953, ECO:0000255|PROSITE- CC ProRule:PRU01383}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AE003852; AAF95191.1; -; Genomic_DNA. DR PIR; E82126; E82126. DR RefSeq; NP_231677.1; NC_002505.1. DR RefSeq; WP_000197425.1; NZ_LT906614.1. DR AlphaFoldDB; Q9KQF5; -. DR SMR; Q9KQF5; -. DR STRING; 243277.VC_2043; -. DR DNASU; 2613424; -. DR EnsemblBacteria; AAF95191; AAF95191; VC_2043. DR KEGG; vch:VC_2043; -. DR PATRIC; fig|243277.26.peg.1951; -. DR eggNOG; COG0550; Bacteria. DR HOGENOM; CLU_002929_5_2_6; -. DR Proteomes; UP000000584; Chromosome 1. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW. DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IEA:UniProtKB-UniRule. DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule. DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule. DR CDD; cd00186; TOP1Ac; 1. DR CDD; cd03362; TOPRIM_TopoIA_TopoIII; 1. DR Gene3D; 3.40.50.140; -; 1. DR Gene3D; 1.10.460.10; Topoisomerase I, domain 2; 1. DR Gene3D; 2.70.20.10; Topoisomerase I, domain 3; 1. DR Gene3D; 1.10.290.10; Topoisomerase I, domain 4; 1. DR HAMAP; MF_00953; Topoisom_3_prok; 1. DR InterPro; IPR000380; Topo_IA. DR InterPro; IPR003601; Topo_IA_2. DR InterPro; IPR023406; Topo_IA_AS. DR InterPro; IPR013497; Topo_IA_cen. DR InterPro; IPR013824; Topo_IA_cen_sub1. DR InterPro; IPR013825; Topo_IA_cen_sub2. DR InterPro; IPR013826; Topo_IA_cen_sub3. DR InterPro; IPR023405; Topo_IA_core_domain. DR InterPro; IPR003602; Topo_IA_DNA-bd_dom. DR InterPro; IPR005738; TopoIII. DR InterPro; IPR006171; TOPRIM_domain. DR InterPro; IPR034144; TOPRIM_TopoIII. DR NCBIfam; TIGR01056; topB; 1. DR PANTHER; PTHR11390:SF21; DNA TOPOISOMERASE 3-ALPHA; 1. DR PANTHER; PTHR11390; PROKARYOTIC DNA TOPOISOMERASE; 1. DR Pfam; PF01131; Topoisom_bac; 1. DR Pfam; PF01751; Toprim; 1. DR PRINTS; PR00417; PRTPISMRASEI. DR SMART; SM00437; TOP1Ac; 1. DR SMART; SM00436; TOP1Bc; 1. DR SMART; SM00493; TOPRIM; 1. DR SUPFAM; SSF56712; Prokaryotic type I DNA topoisomerase; 1. DR PROSITE; PS00396; TOPO_IA_1; 1. DR PROSITE; PS52039; TOPO_IA_2; 1. DR PROSITE; PS50880; TOPRIM; 1. PE 3: Inferred from homology; KW DNA-binding; Isomerase; Magnesium; Metal-binding; Reference proteome; KW Topoisomerase. FT CHAIN 1..647 FT /note="DNA topoisomerase 3" FT /id="PRO_0000145189" FT DOMAIN 2..135 FT /note="Toprim" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT DOMAIN 156..608 FT /note="Topo IA-type catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383" FT REGION 195..200 FT /note="Interaction with DNA" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT ACT_SITE 332 FT /note="O-(5'-phospho-DNA)-tyrosine intermediate" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383" FT BINDING 8 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT BINDING 104 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /ligand_note="catalytic" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT BINDING 104 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT BINDING 106 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT SITE 62 FT /note="Interaction with DNA" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT SITE 171 FT /note="Interaction with DNA" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT SITE 179 FT /note="Interaction with DNA" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" FT SITE 334 FT /note="Interaction with DNA" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953" SQ SEQUENCE 647 AA; 72711 MW; FD90899D8C4CF2C5 CRC64; MTRLFIAEKP SLARAIADAL PKPHKKEQGC IRCANGDIVT WCIGHLLEQV EPDAYDERYK KWNMADLPII PEQWQLRPRK SSSQQLTVVR KLLKEATQII HAGDPDREGQ LLVDEVIDYC KVPKSKKETV QRLLISDLNL SAVKRALQGL RSNREFIPLS VSALARSRAD WLYGMNMSRA YTLLGKKAGY QGVLSVGRVQ TPVLGLVVRR DEEIEHFIPH DYFTLDALIP YQNGTEYFDI RARWKPSEAC LPWQDEEGRV TNRKLVDNVA SRIANQPATV TESEQDQTKQ AAPLPYSLSA LQIDAAKRYN FSAQQVLDLC QSLYEKHKLI TYPRSDCRYL PKEHLAQAPD VVAAIANNAQ EMVTAVNDAD LSLRSKAWND SKVDAHHAII PTPKKASVNA LSGHEMKVYQ LIARQYLMQF YPAAIYAEAK LVFNIAGGIF IAKGRQLLSA GWKVLTGQQD EQEECVDKVP PLPVGIVLQC REGEIKQRQT EPPRHFTEAT LLQAMTGIAR FVADKELKKI LRETDGLGTE ATRAGILDTL FKRGLLQRDN KLIKSTPAGR GLIHALPSEA TYPDMTAHWE HQLQAIAEKG QAYQPFMQTL QGRLEQLIEQ VQVAPVPVSL QALPAVSKPA FKRTRRAPKS KARTYKA //