ID A0A3N4XFU3_9PAST Unreviewed; 639 AA.
AC A0A3N4XFU3;
DT 13-FEB-2019, integrated into UniProtKB/TrEMBL.
DT 13-FEB-2019, sequence version 1.
DT 24-JAN-2024, entry version 23.
DE RecName: Full=DNA topoisomerase 3 {ECO:0000256|HAMAP-Rule:MF_00953};
DE EC=5.6.2.1 {ECO:0000256|HAMAP-Rule:MF_00953};
DE AltName: Full=DNA topoisomerase III {ECO:0000256|HAMAP-Rule:MF_00953};
GN Name=topB {ECO:0000256|HAMAP-Rule:MF_00953};
GN ORFNames=EDC49_0628 {ECO:0000313|EMBL:RPE96240.1};
OS Frederiksenia canicola.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Frederiksenia.
OX NCBI_TaxID=123824 {ECO:0000313|EMBL:RPE96240.1, ECO:0000313|Proteomes:UP000276901};
RN [1] {ECO:0000313|EMBL:RPE96240.1, ECO:0000313|Proteomes:UP000276901}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 25797 {ECO:0000313|EMBL:RPE96240.1,
RC ECO:0000313|Proteomes:UP000276901};
RA Goeker M.;
RT "Genomic Encyclopedia of Type Strains, Phase IV (KMG-IV): sequencing the
RT most valuable type-strain genomes for metagenomic binning, comparative
RT biology and taxonomic classification.";
RL Submitted (NOV-2018) to the EMBL/GenBank/DDBJ databases.
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:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00000213, ECO:0000256|HAMAP-
CC Rule:MF_00953};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00953};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000256|HAMAP-Rule:MF_00953};
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC {ECO:0000256|ARBA:ARBA00009446, ECO:0000256|HAMAP-Rule:MF_00953}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:RPE96240.1}.
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DR EMBL; RKQT01000001; RPE96240.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A3N4XFU3; -.
DR OrthoDB; 9803554at2; -.
DR Proteomes; UP000276901; Unassembled WGS sequence.
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; TOPOISOMERASE_I_PROK; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_00953};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_00953};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00953};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00953};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_00953}.
FT DOMAIN 1..134
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 194..199
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT ACT_SITE 329
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT BINDING 103
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT BINDING 103
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT BINDING 105
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT SITE 61
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT SITE 170
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT SITE 178
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT SITE 185
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
FT SITE 331
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
SQ SEQUENCE 639 AA; 72494 MW; 26DA1A30283BB841 CRC64;
MKLFIAEKPS LGRAIAQVLP KPHHNKDGFI ECGEGNVVTW CIGHLLEQAE PDAYDERFKI
WRMEHLPIVP EQWKLIPKKE TLKQFKVVER LVKQADQLIH AGDPDREGQL LVDEVFGYLN
LPTEKRSQIQ RCLISDLNPS AVQKAVEKLQ SNRDFIPLAT SALARARADW LYGINMTRAY
TLQGRWAGYK GVLSVGRVQT PVLGMIVRRD LEIENFVPKD YFEVLAHIIV PETQERFTAQ
WQPSKACEDY QDDEGRVLSQ PLAENVVKRI ENQPACVIDY QDKIETEIAP LPYSLSALQI
DAARRFGLSA QAVLDICQKL YETHKLITYP RSDNRYLPNE HFAERLKVMA AIAHHLTEYT
EKPEAVDPNR KNRCWNDSKV EAHHAIIPTA RQGNVHLTDN ERRIYQLIAR QYLLQFCPDA
EYRKGKIILN IAGGTFATQA RNLIVAGWKA LLGKEDSDEV AEPLLPLVKK DQQLHCEKGE
IVSKKTQPPR PFSDATLLSA MTGIARFVQD KQLKKVLRET DGLGTEATRA GIIELLFKRG
FLIKKGRSIH STEAGRTLIA ALPETATQPD MTAHWEMQLT DISKKQASYQ QFIADLNKQL
PSLLHSPNRM VLQNLARIIP LVTTSKGQSS RKNVKSAEK
//
