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O73954

- TOP1_PYRFU

UniProt

O73954 - TOP1_PYRFU

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Protein

DNA topoisomerase 1

Gene

topA

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 4 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).By similarity

Catalytic activityi

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

Cofactori

Mg2+By similarityNote: Binds two Mg(2+) per subunit.By similarity

Sites

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

Regions

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

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
  3. endonuclease activity Source: UniProtKB-KW
  4. 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 partPRO_0000034794Add
BLAST
Chaini315 – 687373Endonuclease PI-PfuISequence AnalysisPRO_0000034795Add
BLAST
Chaini688 – 1060373DNA topoisomerase 1, 2nd partPRO_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.Curated

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Proteomic databases

PRIDEiO73954.

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi186497.PF0494.

Structurei

3D structure databases

ProteinModelPortaliO73954.
ModBaseiSearch...
MobiDBiSearch...

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 DNABy similarity

Sequence similaritiesi

Belongs to the type IA topoisomerase family.Curated
Contains 1 Toprim domain.Curated

Zinc finger

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

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_dom.
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

        10         20         30         40         50
MILVIAEKPN VARKIAMALA EVKPIKKTLF GVPYYELIRD GKRLIVASAV
60 70 80 90 100
GHLYGLAPKN DFFGYPIFDV EWVPVYIAEK GKEYAKDYIK LLSVLSKRVR
110 120 130 140 150
EFIVACDYDT EGEVIGYTAL KYACGVDPGV AKRMKFSALT KRDLIKAWYN
160 170 180 190 200
LEPTINFGMA NAGIARHILD WYWGVNLSRA LTHAIKRASG KWVVLSTGRV
210 220 230 240 250
QGPTLKFLVD REREIQSFVP QPYWVIKLIF EKNGKKYTAN YEKDKIWDEN
260 270 280 290 300
EAKRIVLEVK KAPARVTNIE VKQQNRNPPV PFDLGTLQRE AYSAFGFSPK
310 320 330 340 350
KTLDIAQSLY EKGFCLHPDT LILTSQGVRK IKELSREGEV FALDFNLKLS
360 370 380 390 400
KAKYRLLERD ADEQMYKVTL LDGTELYLTA DHPVLVYREG NLAFVPADKL
410 420 430 440 450
RETDHVVLVL NKSARDNYGF LDLLLEITDS QEDYAILENG ETLSLHSLKM
460 470 480 490 500
LVERGEIKDI AVVGFSHNNF GKVMLRDELW YLIGYLAGKG GEIKGNGVVI
510 520 530 540 550
SSRTKEIVGL TKSLNIDLIE TEEGIVLSNK SFVRLLHLIH YTPRVPEVYG
560 570 580 590 600
IINNTEWLKA FLAGYYDATL LEGLTLEALY KIKVYLQLLG IRAKIEDNKL
610 620 630 640 650
KVHLEDLQRF RELLGKFSRR KLYVETSQVP VFTDFDERSY DFPRILGGDI
660 670 680 690 700
YIIGIKSIEK FHYKGKVYDL VVENYHNFIA NGIAVHNCSY PRTESQKLPK
710 720 730 740 750
NLNYKFIIQN LARIPEYRPY AHLLLGMPEL KPVEGKKEDP AHPAIYPTGE
760 770 780 790 800
IPRPGDLTKD EALLYDMIVR RFLAVFMEPA VRETVKVTIS AGKHKFFISG
810 820 830 840 850
GRTVKEGWLR VYGKYVKFDE VTLPTFFIGE RIKVLQVKRE KKKTKPPARY
860 870 880 890 900
SPAAVIKKME DLGLGTKATR AQILETLYQR GYIEGKKSIK VTPLGMKVIE
910 920 930 940 950
TLEKYVPEII SVELTREFEK KMELIMEGKL TKEEVIEEAK IRLTKILEEF
960 970 980 990 1000
KKKELEIGLE LAKIVVGEEK PPLIVGKCPK CGGDLIVKYN EKTGKRFVGC
1010 1020 1030 1040 1050
SNWPKCNVTY PILQRGEIIP TNKTCCNGAP VVIIREKDGR EWEICLDMNC
1060
KEYNTIKKKR
Length:1,060
Mass (Da):121,182
Last modified:September 26, 2001 - v2
Checksum:i81D815333D51C0BC
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti218 – 2181F → L in AAC26106. (PubMed:9524230)Curated
Sequence conflicti235 – 2351K → E in AAC26106. (PubMed:9524230)Curated
Sequence conflicti293 – 2931S → P in AAC26106. (PubMed:9524230)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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_dom.
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: November 26, 2014
This is version 120 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