ID E1VFH2_9GAMM Unreviewed; 672 AA.
AC E1VFH2;
DT 30-NOV-2010, integrated into UniProtKB/TrEMBL.
DT 30-NOV-2010, sequence version 1.
DT 24-JAN-2024, entry version 73.
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 ECO:0000313|EMBL:CBL43615.1};
GN ORFNames=HDN1F_00320 {ECO:0000313|EMBL:CBL43615.1};
OS gamma proteobacterium HdN1.
OC Bacteria; Pseudomonadota; Gammaproteobacteria.
OX NCBI_TaxID=83406 {ECO:0000313|EMBL:CBL43615.1, ECO:0000313|Proteomes:UP000002677};
RN [1] {ECO:0000313|EMBL:CBL43615.1, ECO:0000313|Proteomes:UP000002677}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HdN1 {ECO:0000313|Proteomes:UP000002677};
RA Widdel F., Rabus R., Grundmann O., Werner I., Schreiber F., Ehrenreich P.,
RA Behrends A., Wilkes H., Kube M., Reinhardt R., Zedelius J.;
RT "Alkane degradation by a new type of denitrifying bacterium with possible
RT involvement of the electron acceptor in substrate activation.";
RL Environ. Microbiol. 0:0-0(2010).
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: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00953}.
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DR EMBL; FP929140; CBL43615.1; -; Genomic_DNA.
DR AlphaFoldDB; E1VFH2; -.
DR STRING; 83406.HDN1F_00320; -.
DR KEGG; gpb:HDN1F_00320; -.
DR eggNOG; COG0550; Bacteria.
DR HOGENOM; CLU_002929_5_2_6; -.
DR OrthoDB; 9803554at2; -.
DR Proteomes; UP000002677; Chromosome.
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 Reference proteome {ECO:0000313|Proteomes:UP000002677};
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 REGION 627..672
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 627..641
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 642..656
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 657..672
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 344
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 346
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00953"
SQ SEQUENCE 672 AA; 75155 MW; 89B05BE3915F2FA9 CRC64;
MKLYIAEKPS LARAIAEALP RPHNRQDSCI QLGNGDCVTW CIGHLLEQAE PDAYDAAYKK
WQIAHLPILP EQWQLQPKAS TRKQLSALRT LIQSADQLVH AGDPDREGQL LVDEVIHYFK
VPAAKRRNMQ RLLISDLNPT AVARALTQMR SNQEFTALST SALARSRADW LYGINMTRAY
TLQGQSAGYQ GVLSVGRVQT PVLGLVVRRD QVIANFISVP YYEVLAHLLT PAPSETAPSL
ADPAHPTDSA RFTARWQPSE ACKPWQDDEG RVLNRALAEN VARRITDQPA HVESVEKIPR
KLSPPLPYSL STLQIDAGRR YGMSAQQVLD GCQQLYERHR LITYPRSDSR HLPEDHFAQS
NDVLRAIASF GEPLQSACRH ANPTLRSKAW DNAKVDAHHA IIPTEKPPQT QSLSDVERKL
YEQIARQYVA QFYPAHRYLE TQLALRIAGG LFTASARQVQ EIGWKTLYAR ETGHAEDTDA
LTEIPPLNPG DILHCERGEL QEKQTRPPAH FTDASLLSAM TGVSRFVKDP EIRKILKETD
GLGTEATRAG IIELLLKRGF VQREGKTLRA TPTGTALIEA LPESATLPDM TAQWESALEA
ICQQKIDYHA FIQPLIETLR TLIEQSTQTS PRSFSGLNAP KHTQRTKRKQ PAQRFSKRLK
SKSPASTGFS KK
//
