TOP1_VIBCH
ID TOP1_VIBCH Reviewed; 876 AA.
AC Q9KRB2;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=DNA topoisomerase 1 {ECO:0000255|HAMAP-Rule:MF_00952};
DE EC=5.6.2.1 {ECO:0000255|HAMAP-Rule:MF_00952};
DE AltName: Full=DNA topoisomerase I {ECO:0000255|HAMAP-Rule:MF_00952};
DE AltName: Full=Omega-protein;
DE AltName: Full=Relaxing enzyme;
DE AltName: Full=Swivelase;
DE AltName: Full=Untwisting enzyme;
GN Name=topA {ECO:0000255|HAMAP-Rule:MF_00952}; OrderedLocusNames=VC_1730;
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_00952}.
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_00952};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00952};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_00952};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00952}.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC {ECO:0000255|HAMAP-Rule:MF_00952}.
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; AAF94880.1; -; Genomic_DNA.
DR PIR; B82163; B82163.
DR RefSeq; NP_231366.1; NC_002505.1.
DR RefSeq; WP_000520431.1; NZ_LT906614.1.
DR AlphaFoldDB; Q9KRB2; -.
DR SMR; Q9KRB2; -.
DR STRING; 243277.VC_1730; -.
DR DNASU; 2613735; -.
DR EnsemblBacteria; AAF94880; AAF94880; VC_1730.
DR KEGG; vch:VC_1730; -.
DR PATRIC; fig|243277.26.peg.1655; -.
DR eggNOG; COG0550; Bacteria.
DR HOGENOM; CLU_002929_4_3_6; -.
DR OMA; PECKYTR; -.
DR BioCyc; VCHO:VC1730-MON; -.
DR Proteomes; UP000000584; Chromosome 1.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03363; TOPRIM_TopoIA_TopoI; 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_00952; Topoisom_1_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; IPR013498; Topo_IA_Znf.
DR InterPro; IPR005733; TopoI_bac-type.
DR InterPro; IPR013263; TopoI_Znr_bac.
DR InterPro; IPR028612; Topoisom_1_IA.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034149; TOPRIM_TopoI.
DR PANTHER; PTHR42785; PTHR42785; 1.
DR Pfam; PF08272; Topo_Zn_Ribbon; 2.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF01396; zf-C4_Topoisom; 2.
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; TIGR01051; topA_bact; 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 Repeat; Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..876
FT /note="DNA topoisomerase 1"
FT /id="PRO_0000145171"
FT DOMAIN 3..150
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT ZN_FING 668..695
FT /note="C4-type 1"
FT ZN_FING 717..742
FT /note="C4-type 2"
FT REGION 37..69
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 200..205
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT COMPBIAS 40..59
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 327
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 9
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_00952"
FT BINDING 119
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_00952"
FT BINDING 119
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 121
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 33
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 176
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 177
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 180
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 192
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 329
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 514
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
SQ SEQUENCE 876 AA; 97910 MW; 8A5BC9148CA1B753 CRC64;
MGKSLVIVES PAKAKTINKY LGKDFIVKSS VGHVRDLPTA GQTATPTGKA AAASTKKAST
TDKEQQKREK ERAALIKKMG VDPYHGWQAN YQILPGKEKV VAELQKLAKD ADSVYLATDL
DREGEAIAWH LREIIGGDEK RYKRVVFNEI TKNAIQQAFK QPGELNMDGV NAQQARRFMD
RVVGFMVSPL LWKKVARGLS AGRVQSVAVK LLVEREREIK AFVPEEFWDI NADTLTADKQ
DFRLLVAQKD GLAFKPVNET EALAAVAALN KAQYEVCKRE DKPTTSKPSA PFITSTLQQA
ASTRLGYGVK KTMMLAQRLY EAGYITYMRT DSTNLSAEAV ENLRGYITKH YGEAYLPSQP
NVYGSKQNAQ EAHEAIRPSD VTVTADDLEG MEADAHKLYA LIWNQFVACQ MTPAQYDSTT
VSVKAAEYTL KAKGRILKFD GWTRVQRPLG KNEDQILPPV KVGDSLKLVS LDPKQHFTKP
PARYTEAALV KELEKRGIGR PSTYASIIST IQDRGYVKVD QRRFFAEKMG EIVTDRLDEN
FDDLMNYDFT ARMEEKLDQI AEGEVNWTAV LDEFFADFSR DLETAEQDES LGGMKPNHIV
MTNILCPTCS RPMGIRTAST GVFLGCSGYG LPPKERCKTT INLGDEEGVI NVLEEDVETA
ALRAKKRCPI CETAMDAYLI DDKRKLHVCG NNPNCEGFIV EEGEFKVKGY EGPTVECDKC
GSDMVLKNGR FGKYMGCTND ACKNTRKILK NGEVAPPKEE PVHFPELPCE NSDAYFVLRD
GASGLFFAAS NFPKSRETRA PLVEELKRFA ERLPEKYQYL TSAPAHDPDG LPAVVRFSRK
EKEHYVRTET EGKPSGWMAV YQEGKWLVTD KRKNAK
