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Protein

DNA topoisomerase 1

Gene

topA

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score: 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.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi9Magnesium 1; catalyticUniRule annotation1
Metal bindingi119Magnesium 1; catalyticUniRule annotation1
Metal bindingi119Magnesium 2UniRule annotation1
Metal bindingi121Magnesium 2UniRule annotation1
Active sitei327O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri668 – 695C4-type 1Add BLAST28
Zinc fingeri717 – 742C4-type 2Add BLAST26

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • DNA topoisomerase activity Source: GO_Central
  • DNA topoisomerase type I activity Source: TIGR
  • magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • DNA topological change Source: TIGR
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciVCHO:VC1730-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IUniRule annotation
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topAUniRule annotation
Ordered Locus Names:VC_1730
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000584 Componenti: Chromosome 1

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451711 – 876DNA topoisomerase 1Add BLAST876

Interactioni

Subunit structurei

Monomer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei33Interaction with DNAUniRule annotation1
Sitei176Interaction with DNAUniRule annotation1
Sitei177Interaction with DNAUniRule annotation1
Sitei180Interaction with DNAUniRule annotation1
Sitei192Interaction with DNAUniRule annotation1
Sitei329Interaction with DNAUniRule annotation1
Sitei514Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi243277.VC1730.

Structurei

3D structure databases

ProteinModelPortaliQ9KRB2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 150ToprimUniRule annotationAdd BLAST148

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni200 – 205Interaction with DNAUniRule annotation6

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri668 – 695C4-type 1Add BLAST28
Zinc fingeri717 – 742C4-type 2Add BLAST26

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
KOiK03168.
OMAiVVECDKC.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9KRB2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKSLVIVES PAKAKTINKY LGKDFIVKSS VGHVRDLPTA GQTATPTGKA
60 70 80 90 100
AAASTKKAST TDKEQQKREK ERAALIKKMG VDPYHGWQAN YQILPGKEKV
110 120 130 140 150
VAELQKLAKD ADSVYLATDL DREGEAIAWH LREIIGGDEK RYKRVVFNEI
160 170 180 190 200
TKNAIQQAFK QPGELNMDGV NAQQARRFMD RVVGFMVSPL LWKKVARGLS
210 220 230 240 250
AGRVQSVAVK LLVEREREIK AFVPEEFWDI NADTLTADKQ DFRLLVAQKD
260 270 280 290 300
GLAFKPVNET EALAAVAALN KAQYEVCKRE DKPTTSKPSA PFITSTLQQA
310 320 330 340 350
ASTRLGYGVK KTMMLAQRLY EAGYITYMRT DSTNLSAEAV ENLRGYITKH
360 370 380 390 400
YGEAYLPSQP NVYGSKQNAQ EAHEAIRPSD VTVTADDLEG MEADAHKLYA
410 420 430 440 450
LIWNQFVACQ MTPAQYDSTT VSVKAAEYTL KAKGRILKFD GWTRVQRPLG
460 470 480 490 500
KNEDQILPPV KVGDSLKLVS LDPKQHFTKP PARYTEAALV KELEKRGIGR
510 520 530 540 550
PSTYASIIST IQDRGYVKVD QRRFFAEKMG EIVTDRLDEN FDDLMNYDFT
560 570 580 590 600
ARMEEKLDQI AEGEVNWTAV LDEFFADFSR DLETAEQDES LGGMKPNHIV
610 620 630 640 650
MTNILCPTCS RPMGIRTAST GVFLGCSGYG LPPKERCKTT INLGDEEGVI
660 670 680 690 700
NVLEEDVETA ALRAKKRCPI CETAMDAYLI DDKRKLHVCG NNPNCEGFIV
710 720 730 740 750
EEGEFKVKGY EGPTVECDKC GSDMVLKNGR FGKYMGCTND ACKNTRKILK
760 770 780 790 800
NGEVAPPKEE PVHFPELPCE NSDAYFVLRD GASGLFFAAS NFPKSRETRA
810 820 830 840 850
PLVEELKRFA ERLPEKYQYL TSAPAHDPDG LPAVVRFSRK EKEHYVRTET
860 870
EGKPSGWMAV YQEGKWLVTD KRKNAK
Length:876
Mass (Da):97,910
Last modified:October 1, 2000 - v1
Checksum:i8A5BC9148CA1B753
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF94880.1.
PIRiB82163.
RefSeqiNP_231366.1. NC_002505.1.
WP_000520431.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF94880; AAF94880; VC_1730.
GeneIDi2613735.
KEGGivch:VC1730.
PATRICi20082518. VBIVibCho83274_1655.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF94880.1.
PIRiB82163.
RefSeqiNP_231366.1. NC_002505.1.
WP_000520431.1. NC_002505.1.

3D structure databases

ProteinModelPortaliQ9KRB2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC1730.

Protocols and materials databases

DNASUi2613735.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF94880; AAF94880; VC_1730.
GeneIDi2613735.
KEGGivch:VC1730.
PATRICi20082518. VBIVibCho83274_1655.

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
KOiK03168.
OMAiVVECDKC.

Enzyme and pathway databases

BioCyciVCHO:VC1730-MONOMER.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTOP1_VIBCH
AccessioniPrimary (citable) accession number: Q9KRB2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: October 1, 2000
Last modified: October 5, 2016
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.