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Protein

DNA topoisomerase 3

Gene

topB

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score: Annotation score: 3 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi8 – 81Magnesium 1; catalyticUniRule annotation
Sitei62 – 621Interaction with DNAUniRule annotation
Metal bindingi104 – 1041Magnesium 1; catalyticUniRule annotation
Metal bindingi104 – 1041Magnesium 2UniRule annotation
Metal bindingi106 – 1061Magnesium 2UniRule annotation
Sitei171 – 1711Interaction with DNAUniRule annotation
Sitei179 – 1791Interaction with DNAUniRule annotation
Active sitei332 – 3321O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei334 – 3341Interaction with DNAUniRule annotation

GO - Molecular functioni

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

GO - Biological processi

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

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciVCHO:VC2043-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 3UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IIIUniRule annotation
Gene namesi
Name:topBUniRule annotation
Ordered Locus Names:VC_2043
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000000584: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 647647DNA topoisomerase 3PRO_0000145189Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi243277.VC2043.

Structurei

3D structure databases

ProteinModelPortaliQ9KQF5.
SMRiQ9KQF5. Positions 3-616.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 135134ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni195 – 2006Interaction with DNAUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0550.
KOiK03169.
OMAiGLIARQY.
OrthoDBiEOG60CWM6.

Family and domain databases

Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00953. Topoisom_3_prok.
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.
IPR005738. TopoIII.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01056. topB. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9KQF5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRLFIAEKP SLARAIADAL PKPHKKEQGC IRCANGDIVT WCIGHLLEQV
60 70 80 90 100
EPDAYDERYK KWNMADLPII PEQWQLRPRK SSSQQLTVVR KLLKEATQII
110 120 130 140 150
HAGDPDREGQ LLVDEVIDYC KVPKSKKETV QRLLISDLNL SAVKRALQGL
160 170 180 190 200
RSNREFIPLS VSALARSRAD WLYGMNMSRA YTLLGKKAGY QGVLSVGRVQ
210 220 230 240 250
TPVLGLVVRR DEEIEHFIPH DYFTLDALIP YQNGTEYFDI RARWKPSEAC
260 270 280 290 300
LPWQDEEGRV TNRKLVDNVA SRIANQPATV TESEQDQTKQ AAPLPYSLSA
310 320 330 340 350
LQIDAAKRYN FSAQQVLDLC QSLYEKHKLI TYPRSDCRYL PKEHLAQAPD
360 370 380 390 400
VVAAIANNAQ EMVTAVNDAD LSLRSKAWND SKVDAHHAII PTPKKASVNA
410 420 430 440 450
LSGHEMKVYQ LIARQYLMQF YPAAIYAEAK LVFNIAGGIF IAKGRQLLSA
460 470 480 490 500
GWKVLTGQQD EQEECVDKVP PLPVGIVLQC REGEIKQRQT EPPRHFTEAT
510 520 530 540 550
LLQAMTGIAR FVADKELKKI LRETDGLGTE ATRAGILDTL FKRGLLQRDN
560 570 580 590 600
KLIKSTPAGR GLIHALPSEA TYPDMTAHWE HQLQAIAEKG QAYQPFMQTL
610 620 630 640
QGRLEQLIEQ VQVAPVPVSL QALPAVSKPA FKRTRRAPKS KARTYKA
Length:647
Mass (Da):72,711
Last modified:October 1, 2000 - v1
Checksum:iFD90899D8C4CF2C5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF95191.1.
PIRiE82126.
RefSeqiNP_231677.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF95191; AAF95191; VC_2043.
GeneIDi2613424.
KEGGivch:VC2043.
PATRICi20083118. VBIVibCho83274_1951.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003852 Genomic DNA. Translation: AAF95191.1.
PIRiE82126.
RefSeqiNP_231677.1. NC_002505.1.

3D structure databases

ProteinModelPortaliQ9KQF5.
SMRiQ9KQF5. Positions 3-616.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC2043.

Protocols and materials databases

DNASUi2613424.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF95191; AAF95191; VC_2043.
GeneIDi2613424.
KEGGivch:VC2043.
PATRICi20083118. VBIVibCho83274_1951.

Phylogenomic databases

eggNOGiCOG0550.
KOiK03169.
OMAiGLIARQY.
OrthoDBiEOG60CWM6.

Enzyme and pathway databases

BioCyciVCHO:VC2043-MONOMER.

Family and domain databases

Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00953. Topoisom_3_prok.
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.
IPR005738. TopoIII.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01056. topB. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 39315 / El Tor Inaba N16961.

Entry informationi

Entry nameiTOP3_VIBCH
AccessioniPrimary (citable) accession number: Q9KQF5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: October 1, 2000
Last modified: January 7, 2015
This is version 97 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

External Data

Dasty 3

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 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.