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O73954 (TOP1_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 116. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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:

  1. Endonuclease PI-PfuI
    EC=3.1.-.-
    Alternative name(s):
    Pfu topA intein
Gene names
Name:topA
Ordered Locus Names:PF0494
OrganismPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]
Taxonomic identifier186497 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

Protein attributes

Sequence length1060 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

Function

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. HAMAP-Rule MF_00952

Catalytic activity

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. HAMAP-Rule MF_00952

Cofactor

Magnesium. Binds two Mg2+ per subunit By similarity. HAMAP-Rule MF_00952

Subunit structure

Monomer By similarity. HAMAP-Rule MF_00952

Post-translational modification

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation Potential. HAMAP-Rule MF_00952

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.

Sequence similarities

Belongs to the type IA topoisomerase family.

Contains 1 DOD-type homing endonuclease domain.

Contains 1 Toprim domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 314314DNA topoisomerase 1, 1st part HAMAP-Rule MF_00952
PRO_0000034794
Chain315 – 687373Endonuclease PI-PfuI Potential
PRO_0000034795
Chain688 – 1060373DNA topoisomerase 1, 2nd part HAMAP-Rule MF_00952
PRO_0000034796

Regions

Domain1 – 141141Toprim
Domain482 – 591110DOD-type homing endonuclease
Zinc finger978 – 100629C4-type 1 HAMAP-Rule MF_00952
Zinc finger1025 – 105026C4-type 2; atypical HAMAP-Rule MF_00952
Region196 – 2016Interaction with DNA By similarity

Sites

Active site6901O-(5'-phospho-DNA)-tyrosine intermediate By similarity
Metal binding71Magnesium 1; catalytic By similarity
Metal binding1071Magnesium 1; catalytic By similarity
Metal binding1071Magnesium 2 By similarity
Metal binding1091Magnesium 2 By similarity
Site521Interaction with DNA By similarity
Site1661Interaction with DNA By similarity
Site1701Interaction with DNA By similarity
Site6921Interaction with DNA By similarity
Site8801Interaction with DNA By similarity

Experimental info

Sequence conflict2181F → L in AAC26106. Ref.2
Sequence conflict2351K → E in AAC26106. Ref.2
Sequence conflict2931S → P in AAC26106. Ref.2

Sequences

Sequence LengthMass (Da)Tools
O73954 [UniParc].

Last modified September 26, 2001. Version 2.
Checksum: 81D815333D51C0BC

FASTA1,060121,182
        10         20         30         40         50         60 
MILVIAEKPN VARKIAMALA EVKPIKKTLF GVPYYELIRD GKRLIVASAV GHLYGLAPKN 

        70         80         90        100        110        120 
DFFGYPIFDV EWVPVYIAEK GKEYAKDYIK LLSVLSKRVR EFIVACDYDT EGEVIGYTAL 

       130        140        150        160        170        180 
KYACGVDPGV AKRMKFSALT KRDLIKAWYN LEPTINFGMA NAGIARHILD WYWGVNLSRA 

       190        200        210        220        230        240 
LTHAIKRASG KWVVLSTGRV QGPTLKFLVD REREIQSFVP QPYWVIKLIF EKNGKKYTAN 

       250        260        270        280        290        300 
YEKDKIWDEN EAKRIVLEVK KAPARVTNIE VKQQNRNPPV PFDLGTLQRE AYSAFGFSPK 

       310        320        330        340        350        360 
KTLDIAQSLY EKGFCLHPDT LILTSQGVRK IKELSREGEV FALDFNLKLS KAKYRLLERD 

       370        380        390        400        410        420 
ADEQMYKVTL LDGTELYLTA DHPVLVYREG NLAFVPADKL RETDHVVLVL NKSARDNYGF 

       430        440        450        460        470        480 
LDLLLEITDS QEDYAILENG ETLSLHSLKM LVERGEIKDI AVVGFSHNNF GKVMLRDELW 

       490        500        510        520        530        540 
YLIGYLAGKG GEIKGNGVVI SSRTKEIVGL TKSLNIDLIE TEEGIVLSNK SFVRLLHLIH 

       550        560        570        580        590        600 
YTPRVPEVYG IINNTEWLKA FLAGYYDATL LEGLTLEALY KIKVYLQLLG IRAKIEDNKL 

       610        620        630        640        650        660 
KVHLEDLQRF RELLGKFSRR KLYVETSQVP VFTDFDERSY DFPRILGGDI YIIGIKSIEK 

       670        680        690        700        710        720 
FHYKGKVYDL VVENYHNFIA NGIAVHNCSY PRTESQKLPK NLNYKFIIQN LARIPEYRPY 

       730        740        750        760        770        780 
AHLLLGMPEL KPVEGKKEDP AHPAIYPTGE IPRPGDLTKD EALLYDMIVR RFLAVFMEPA 

       790        800        810        820        830        840 
VRETVKVTIS AGKHKFFISG GRTVKEGWLR VYGKYVKFDE VTLPTFFIGE RIKVLQVKRE 

       850        860        870        880        890        900 
KKKTKPPARY SPAAVIKKME DLGLGTKATR AQILETLYQR GYIEGKKSIK VTPLGMKVIE 

       910        920        930        940        950        960 
TLEKYVPEII SVELTREFEK KMELIMEGKL TKEEVIEEAK IRLTKILEEF KKKELEIGLE 

       970        980        990       1000       1010       1020 
LAKIVVGEEK PPLIVGKCPK CGGDLIVKYN EKTGKRFVGC SNWPKCNVTY PILQRGEIIP 

      1030       1040       1050       1060 
TNKTCCNGAP VVIIREKDGR EWEICLDMNC KEYNTIKKKR 

« Hide

References

« Hide 'large scale' references
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE009950 Genomic DNA. Translation: AAL80618.1.
AF042825 Genomic DNA. Translation: AAC26106.1.
RefSeqNP_578223.1. NC_003413.1.

3D structure databases

ProteinModelPortalO73954.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING186497.PF0494.

Proteomic databases

PRIDEO73954.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL80618; AAL80618; PF0494.
GeneID1468335.
KEGGpfu:PF0494.

Phylogenomic databases

eggNOGCOG0551.
HOGENOMHOG000004019.
KOK03168.
OMADYHNFIA.

Family and domain databases

Gene3D1.10.290.10. 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.
HAMAPMF_00952. Topoisom_1_prok.
InterProIPR028992. 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]
PANTHERPTHR11390. PTHR11390. 1 hit.
PfamPF01131. Topoisom_bac. 2 hits.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSPR00379. INTEIN.
PR00417. PRTPISMRASEI.
SMARTSM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMSSF51294. SSF51294. 3 hits.
SSF56712. SSF56712. 2 hits.
TIGRFAMsTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
TIGR01057. topA_arch. 2 hits.
PROSITEPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameTOP1_PYRFU
AccessionPrimary (citable) accession number: O73954
Entry history
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: September 26, 2001
Last modified: July 9, 2014
This is version 116 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Intein-containing proteins

List of intein-containing protein entries