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O73954

- TOP1_PYRFU

UniProt

O73954 - TOP1_PYRFU

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Protein

DNA topoisomerase 1

Gene
topA, PF0494
Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 5 out of 5 - Protein inferred from homologyi

Functioni

Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone By similarity.UniRule annotation

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotation

Cofactori

Magnesium. Binds two Mg2+ per subunit By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Magnesium 1; catalytic By similarity
Sitei52 – 521Interaction with DNA By similarity
Metal bindingi107 – 1071Magnesium 1; catalytic By similarity
Metal bindingi107 – 1071Magnesium 2 By similarity
Metal bindingi109 – 1091Magnesium 2 By similarity
Sitei166 – 1661Interaction with DNA By similarity
Sitei170 – 1701Interaction with DNA By similarity
Active sitei690 – 6901O-(5'-phospho-DNA)-tyrosine intermediate By similarity
Sitei692 – 6921Interaction with DNA By similarity
Sitei880 – 8801Interaction with DNA By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri978 – 100629C4-type 1UniRule annotationAdd
BLAST
Zinc fingeri1025 – 105026C4-type 2; atypicalUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: UniProtKB-KW
  3. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
  4. endonuclease activity Source: UniProtKB-KW
  5. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA topological change Source: UniProtKB-HAMAP
  2. intein-mediated protein splicing Source: InterPro
  3. intron homing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Isomerase, Nuclease, Topoisomerase

Keywords - Biological processi

Intron homing

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase I
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Cleaved into the following chain:
Alternative name(s):
Pfu topA intein
Gene namesi
Name:topA
Ordered Locus Names:PF0494
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000001013: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. chromosome Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 314314DNA topoisomerase 1, 1st partUniRule annotationPRO_0000034794Add
BLAST
Chaini315 – 687373Endonuclease PI-PfuI Reviewed predictionPRO_0000034795Add
BLAST
Chaini688 – 1060373DNA topoisomerase 1, 2nd partUniRule annotationPRO_0000034796Add
BLAST

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Reviewed prediction.UniRule annotation

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Proteomic databases

PRIDEiO73954.

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi186497.PF0494.

Structurei

3D structure databases

ProteinModelPortaliO73954.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 141141ToprimAdd
BLAST
Domaini482 – 591110DOD-type homing endonucleaseAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni196 – 2016Interaction with DNA By similarity

Sequence similaritiesi

Contains 1 Toprim domain.

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000004019.
KOiK03168.
OMAiDYHNFIA.

Family and domain databases

Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
2.170.16.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok.
InterProiIPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR013826. Topo_IA_cen_sub3.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd.
IPR013498. Topo_IA_Znf.
IPR005739. TopoI_arch.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSiPR00379. INTEIN.
PR00417. PRTPISMRASEI.
SMARTiSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 3 hits.
SSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
TIGR01057. topA_arch. 2 hits.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O73954-1 [UniParc]FASTAAdd to Basket

« Hide

MILVIAEKPN VARKIAMALA EVKPIKKTLF GVPYYELIRD GKRLIVASAV     50
GHLYGLAPKN DFFGYPIFDV EWVPVYIAEK GKEYAKDYIK LLSVLSKRVR 100
EFIVACDYDT EGEVIGYTAL KYACGVDPGV AKRMKFSALT KRDLIKAWYN 150
LEPTINFGMA NAGIARHILD WYWGVNLSRA LTHAIKRASG KWVVLSTGRV 200
QGPTLKFLVD REREIQSFVP QPYWVIKLIF EKNGKKYTAN YEKDKIWDEN 250
EAKRIVLEVK KAPARVTNIE VKQQNRNPPV PFDLGTLQRE AYSAFGFSPK 300
KTLDIAQSLY EKGFCLHPDT LILTSQGVRK IKELSREGEV FALDFNLKLS 350
KAKYRLLERD ADEQMYKVTL LDGTELYLTA DHPVLVYREG NLAFVPADKL 400
RETDHVVLVL NKSARDNYGF LDLLLEITDS QEDYAILENG ETLSLHSLKM 450
LVERGEIKDI AVVGFSHNNF GKVMLRDELW YLIGYLAGKG GEIKGNGVVI 500
SSRTKEIVGL TKSLNIDLIE TEEGIVLSNK SFVRLLHLIH YTPRVPEVYG 550
IINNTEWLKA FLAGYYDATL LEGLTLEALY KIKVYLQLLG IRAKIEDNKL 600
KVHLEDLQRF RELLGKFSRR KLYVETSQVP VFTDFDERSY DFPRILGGDI 650
YIIGIKSIEK FHYKGKVYDL VVENYHNFIA NGIAVHNCSY PRTESQKLPK 700
NLNYKFIIQN LARIPEYRPY AHLLLGMPEL KPVEGKKEDP AHPAIYPTGE 750
IPRPGDLTKD EALLYDMIVR RFLAVFMEPA VRETVKVTIS AGKHKFFISG 800
GRTVKEGWLR VYGKYVKFDE VTLPTFFIGE RIKVLQVKRE KKKTKPPARY 850
SPAAVIKKME DLGLGTKATR AQILETLYQR GYIEGKKSIK VTPLGMKVIE 900
TLEKYVPEII SVELTREFEK KMELIMEGKL TKEEVIEEAK IRLTKILEEF 950
KKKELEIGLE LAKIVVGEEK PPLIVGKCPK CGGDLIVKYN EKTGKRFVGC 1000
SNWPKCNVTY PILQRGEIIP TNKTCCNGAP VVIIREKDGR EWEICLDMNC 1050
KEYNTIKKKR 1060
Length:1,060
Mass (Da):121,182
Last modified:September 26, 2001 - v2
Checksum:i81D815333D51C0BC
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti218 – 2181F → L in AAC26106. 1 Publication
Sequence conflicti235 – 2351K → E in AAC26106. 1 Publication
Sequence conflicti293 – 2931S → P in AAC26106. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE009950 Genomic DNA. Translation: AAL80618.1.
AF042825 Genomic DNA. Translation: AAC26106.1.
RefSeqiNP_578223.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL80618; AAL80618; PF0494.
GeneIDi1468335.
KEGGipfu:PF0494.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE009950 Genomic DNA. Translation: AAL80618.1 .
AF042825 Genomic DNA. Translation: AAC26106.1 .
RefSeqi NP_578223.1. NC_003413.1.

3D structure databases

ProteinModelPortali O73954.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 186497.PF0494.

Proteomic databases

PRIDEi O73954.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL80618 ; AAL80618 ; PF0494 .
GeneIDi 1468335.
KEGGi pfu:PF0494.

Phylogenomic databases

eggNOGi COG0551.
HOGENOMi HOG000004019.
KOi K03168.
OMAi DYHNFIA.

Family and domain databases

Gene3Di 1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
2.170.16.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPi MF_00952. Topoisom_1_prok.
InterProi IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR013826. Topo_IA_cen_sub3.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd.
IPR013498. Topo_IA_Znf.
IPR005739. TopoI_arch.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami PF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view ]
PRINTSi PR00379. INTEIN.
PR00417. PRTPISMRASEI.
SMARTi SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view ]
SUPFAMi SSF51294. SSF51294. 3 hits.
SSF56712. SSF56712. 2 hits.
TIGRFAMsi TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
TIGR01057. topA_arch. 2 hits.
PROSITEi PS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
    Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
    Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
  2. "A topA intein in Pyrococcus furiosus and its relatedness to the r-gyr intein of Methanococcus jannaschii."
    Chute I.C., Hu Z., Liu X.-Q.
    Gene 210:85-92(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 127-1060.

Entry informationi

Entry nameiTOP1_PYRFU
AccessioniPrimary (citable) accession number: O73954
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: September 26, 2001
Last modified: September 3, 2014
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

When a topoisomerase transiently breaks a DNA backbone bond, it simultaneously forms a protein-DNA link, in which a tyrosyl oxygen in the enzyme is joined to a DNA phosphorus at one end of the enzyme-severed DNA strand.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi