TOP1_PYRFU
ID TOP1_PYRFU Reviewed; 1060 AA.
AC O73954;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 26-SEP-2001, sequence version 2.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=DNA topoisomerase 1;
DE EC=5.6.2.1;
DE AltName: Full=DNA topoisomerase I;
DE AltName: Full=Omega-protein;
DE AltName: Full=Relaxing enzyme;
DE AltName: Full=Swivelase;
DE AltName: Full=Untwisting enzyme;
DE Contains:
DE RecName: Full=Endonuclease PI-PfuI;
DE EC=3.1.-.-;
DE AltName: Full=Pfu topA intein;
GN Name=topA; OrderedLocusNames=PF0494;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 127-1060.
RX PubMed=9524230; DOI=10.1016/s0378-1119(98)00044-4;
RA Chute I.C., Hu Z., Liu X.-Q.;
RT "A topA intein in Pyrococcus furiosus and its relatedness to the r-gyr
RT intein of Methanococcus jannaschii.";
RL Gene 210:85-92(1998).
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 (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-independent breakage of single-stranded DNA, followed by
CC passage and rejoining.; EC=5.6.2.1;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000250};
CC -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- PTM: This protein undergoes a protein self splicing that involves a
CC post-translational excision of the intervening region (intein) followed
CC by peptide ligation. {ECO:0000305}.
CC -!- MISCELLANEOUS: When a topoisomerase transiently breaks a DNA backbone
CC bond, it simultaneously forms a protein-DNA link, in which a tyrosyl
CC oxygen in the enzyme is joined to a DNA phosphorus at one end of the
CC enzyme-severed DNA strand.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family. {ECO:0000305}.
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DR EMBL; AE009950; AAL80618.1; -; Genomic_DNA.
DR EMBL; AF042825; AAC26106.1; -; Genomic_DNA.
DR RefSeq; WP_011011611.1; NZ_CP023154.1.
DR AlphaFoldDB; O73954; -.
DR STRING; 186497.PF0494; -.
DR PRIDE; O73954; -.
DR EnsemblBacteria; AAL80618; AAL80618; PF0494.
DR GeneID; 41712296; -.
DR KEGG; pfu:PF0494; -.
DR PATRIC; fig|186497.12.peg.517; -.
DR eggNOG; arCOG01527; Archaea.
DR eggNOG; arCOG03151; Archaea.
DR HOGENOM; CLU_002929_5_5_2; -.
DR OMA; DYHNFIA; -.
DR OrthoDB; 14543at2157; -.
DR PhylomeDB; O73954; -.
DR Proteomes; UP000001013; 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:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0016539; P:intein-mediated protein splicing; IEA:InterPro.
DR GO; GO:0006314; P:intron homing; IEA:UniProtKB-KW.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03362; TOPRIM_TopoIA_TopoIII; 1.
DR Gene3D; 1.10.290.10; -; 2.
DR Gene3D; 1.10.460.10; -; 2.
DR Gene3D; 2.70.20.10; -; 1.
DR HAMAP; MF_00952; Topoisom_1_prok; 1.
DR InterPro; IPR003586; Hint_dom_C.
DR InterPro; IPR003587; Hint_dom_N.
DR InterPro; IPR036844; Hint_dom_sf.
DR InterPro; IPR006142; INTEIN.
DR InterPro; IPR030934; Intein_C.
DR InterPro; IPR004042; Intein_endonuc.
DR InterPro; IPR006141; Intein_N.
DR InterPro; IPR000380; Topo_IA.
DR InterPro; IPR003601; Topo_IA_2.
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; 2.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF01396; zf-C4_Topoisom; 1.
DR PRINTS; PR00379; INTEIN.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00305; HintC; 1.
DR SMART; SM00306; HintN; 1.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SUPFAM; SSF51294; SSF51294; 1.
DR SUPFAM; SSF56712; SSF56712; 2.
DR TIGRFAMs; TIGR01443; intein_Cterm; 1.
DR TIGRFAMs; TIGR01445; intein_Nterm; 1.
DR TIGRFAMs; TIGR01057; topA_arch; 2.
DR PROSITE; PS50818; INTEIN_C_TER; 1.
DR PROSITE; PS50819; INTEIN_ENDONUCLEASE; 1.
DR PROSITE; PS50817; INTEIN_N_TER; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW Autocatalytic cleavage; DNA-binding; Endonuclease; Hydrolase;
KW Intron homing; Isomerase; Magnesium; Metal-binding; Nuclease;
KW Protein splicing; Reference proteome; Repeat; Topoisomerase; Zinc;
KW Zinc-finger.
FT CHAIN 1..314
FT /note="DNA topoisomerase 1, 1st part"
FT /id="PRO_0000034794"
FT CHAIN 315..687
FT /note="Endonuclease PI-PfuI"
FT /evidence="ECO:0000255"
FT /id="PRO_0000034795"
FT CHAIN 688..1060
FT /note="DNA topoisomerase 1, 2nd part"
FT /id="PRO_0000034796"
FT DOMAIN 1..141
FT /note="Toprim"
FT DOMAIN 482..591
FT /note="DOD-type homing endonuclease"
FT ZN_FING 978..1006
FT /note="C4-type 1"
FT ZN_FING 1025..1050
FT /note="C4-type 2; atypical"
FT REGION 196..201
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT ACT_SITE 690
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000250"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 107
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 107
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 109
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT SITE 52
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 166
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 170
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 692
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT SITE 880
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250"
FT CONFLICT 218
FT /note="F -> L (in Ref. 2; AAC26106)"
FT /evidence="ECO:0000305"
FT CONFLICT 235
FT /note="K -> E (in Ref. 2; AAC26106)"
FT /evidence="ECO:0000305"
FT CONFLICT 293
FT /note="S -> P (in Ref. 2; AAC26106)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1060 AA; 121182 MW; 81D815333D51C0BC CRC64;
MILVIAEKPN VARKIAMALA EVKPIKKTLF GVPYYELIRD GKRLIVASAV GHLYGLAPKN
DFFGYPIFDV EWVPVYIAEK GKEYAKDYIK LLSVLSKRVR EFIVACDYDT EGEVIGYTAL
KYACGVDPGV AKRMKFSALT KRDLIKAWYN LEPTINFGMA NAGIARHILD WYWGVNLSRA
LTHAIKRASG KWVVLSTGRV QGPTLKFLVD REREIQSFVP QPYWVIKLIF EKNGKKYTAN
YEKDKIWDEN EAKRIVLEVK KAPARVTNIE VKQQNRNPPV PFDLGTLQRE AYSAFGFSPK
KTLDIAQSLY EKGFCLHPDT LILTSQGVRK IKELSREGEV FALDFNLKLS KAKYRLLERD
ADEQMYKVTL LDGTELYLTA DHPVLVYREG NLAFVPADKL RETDHVVLVL NKSARDNYGF
LDLLLEITDS QEDYAILENG ETLSLHSLKM LVERGEIKDI AVVGFSHNNF GKVMLRDELW
YLIGYLAGKG GEIKGNGVVI SSRTKEIVGL TKSLNIDLIE TEEGIVLSNK SFVRLLHLIH
YTPRVPEVYG IINNTEWLKA FLAGYYDATL LEGLTLEALY KIKVYLQLLG IRAKIEDNKL
KVHLEDLQRF RELLGKFSRR KLYVETSQVP VFTDFDERSY DFPRILGGDI YIIGIKSIEK
FHYKGKVYDL VVENYHNFIA NGIAVHNCSY PRTESQKLPK NLNYKFIIQN LARIPEYRPY
AHLLLGMPEL KPVEGKKEDP AHPAIYPTGE IPRPGDLTKD EALLYDMIVR RFLAVFMEPA
VRETVKVTIS AGKHKFFISG GRTVKEGWLR VYGKYVKFDE VTLPTFFIGE RIKVLQVKRE
KKKTKPPARY SPAAVIKKME DLGLGTKATR AQILETLYQR GYIEGKKSIK VTPLGMKVIE
TLEKYVPEII SVELTREFEK KMELIMEGKL TKEEVIEEAK IRLTKILEEF KKKELEIGLE
LAKIVVGEEK PPLIVGKCPK CGGDLIVKYN EKTGKRFVGC SNWPKCNVTY PILQRGEIIP
TNKTCCNGAP VVIIREKDGR EWEICLDMNC KEYNTIKKKR
