TOP1_PYRAB
ID TOP1_PYRAB Reviewed; 685 AA.
AC Q9UYS8; G8ZHN7;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 141.
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=PYRAB14290;
GN ORFNames=PAB1430;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
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}.
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DR EMBL; AJ248287; CAB50334.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE70874.1; -; Genomic_DNA.
DR PIR; A75055; A75055.
DR RefSeq; WP_010868544.1; NC_000868.1.
DR AlphaFoldDB; Q9UYS8; -.
DR SMR; Q9UYS8; -.
DR STRING; 272844.PAB1430; -.
DR EnsemblBacteria; CAB50334; CAB50334; PAB1430.
DR GeneID; 1496820; -.
DR KEGG; pab:PAB1430; -.
DR PATRIC; fig|272844.11.peg.1519; -.
DR eggNOG; arCOG01527; Archaea.
DR HOGENOM; CLU_002929_5_2_2; -.
DR OMA; PECKYTR; -.
DR OrthoDB; 14543at2157; -.
DR PhylomeDB; Q9UYS8; -.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
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; 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_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; IPR005739; TopoI_arch.
DR InterPro; IPR028612; Topoisom_1_IA.
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 Pfam; PF01396; zf-C4_Topoisom; 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; TIGR01057; topA_arch; 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; Repeat; Topoisomerase;
KW Zinc; Zinc-finger.
FT CHAIN 1..685
FT /note="DNA topoisomerase 1"
FT /id="PRO_0000145180"
FT DOMAIN 1..141
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT ZN_FING 611..639
FT /note="C4-type 1"
FT ZN_FING 658..682
FT /note="C4-type 2; atypical"
FT REGION 196..201
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT ACT_SITE 317
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 7
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 107
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 107
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 109
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 52
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 166
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 170
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 319
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 507
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
SQ SEQUENCE 685 AA; 78196 MW; 4888C43AB87B485D CRC64;
MILVIAEKPN VARKIAGALS ERRPIRKTIF GVPYYEVFRD GKKLIVASAV GHLYGLAPKQ
DFFGYPIFDI EWVPVYIAEK NKDYAKDYIK ALSVLAKRVK EFIVACDYDT EGEVIGYTAL
KYACGVDPSR AKRMKFSALT KRDLLNAWRN LEPTINFGMA NAGIARHVLD WYWGVNLSRA
LTHAIKRASG KWVVLSTGRV QGPTLKFLVE REREIQSFVP KPYWVIKLVI EKNGQKLVAN
YEKDKIWSEE EAKKIVTEVK KSKARVSNIE VKRQKRNPPV PFDLGTLQRE AYSAFGFSPK
KTLDIAQSLY EKGFTSYPRT ESQKLPKNLN FRLIIQNISR MPQYRPYAHL LLGMPELKPV
EGKKEDPAHP AIYPTGEIPG PGDLSKDEEK LYDMIVRRFL ALFMEPAVRE SVKVTILAGP
HKFMLSGART VKQGWLSVYG KYIKFDEVTL PEFFIGERVR VLQVRREKKK TKPPARYSPA
AVIKKMEDLG IGTKATRAQI LETLYQRGYI EGKKSIKVTP LGMKVIETLE KYVPEIISVE
LTREFERKMD LIMQGKLTKE EVIEEAKVKL TKILEEFKKR ELEIGLELAR IVVGDVKDEI
KEEKPIVVGK CPKCGGDLIV KYNKKTGKRF VGCSNWPKCD VTYPILQRGE IIPTNKTCCN
GAPVVIIRDK GRDIEICLDI KCKKW
