TOP3_VIBCH
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 03-AUG-2022, entry version 125.
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}; OrderedLocusNames=VC_2043;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; 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;
CC Evidence={ECO:0000255|HAMAP-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}.
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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 OMA; TYPRVDT; -.
DR BioCyc; VCHO:VC2043-MON; -.
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; 1.10.290.10; -; 1.
DR Gene3D; 1.10.460.10; -; 1.
DR Gene3D; 2.70.20.10; -; 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 PANTHER; PTHR11390; PTHR11390; 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; SSF56712; 1.
DR TIGRFAMs; TIGR01056; topB; 1.
DR PROSITE; PS00396; TOPOISOMERASE_I_PROK; 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 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|HAMAP-Rule:MF_00953"
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
