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Protein

DNA topoisomerase 3

Gene

topB

Organism
Dickeya dadantii (strain Ech703)
Status
Unreviewed-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 annotationSAAS annotation

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Magnesium 1; catalyticUniRule annotation
Metal bindingi103 – 1031Magnesium 1; catalyticUniRule annotation
Metal bindingi103 – 1031Magnesium 2UniRule annotation
Metal bindingi105 – 1051Magnesium 2UniRule annotation
Active sitei328 – 3281O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, TopoisomeraseUniRule annotationSAAS annotation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotation, Metal-bindingUniRule annotation

Enzyme and pathway databases

BioCyciDDAD579405:GHJU-2007-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:Dd703_1966Imported
OrganismiDickeya dadantii (strain Ech703)Imported
Taxonomic identifieri579405 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeDickeya
Proteomesi
  • UP000002734 Componenti: Chromosome

Interactioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei61 – 611Interaction with DNAUniRule annotation
Sitei170 – 1701Interaction with DNAUniRule annotation
Sitei178 – 1781Interaction with DNAUniRule annotation
Sitei185 – 1851Interaction with DNAUniRule annotation
Sitei330 – 3301Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi579405.Dd703_1966.

Structurei

3D structure databases

ProteinModelPortaliC6C5W5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 134134ToprimInterPro annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni194 – 1996Interaction with DNAUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
KOiK03169.
OMAiSTYPDMT.
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. 2 hits.
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.

C6C5W5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLFIAEKPS LARAIADVLP KPQRRGEGFI ACGQHDVVTW CVGHLLEQAE
60 70 80 90 100
PERYDPRYAR WTLADLPIVP QKWLLQPRPS VSKQLKAIGQ LLKQADEIVH
110 120 130 140 150
AGDPDREGQL LVDEVLEYLA LSEEKRGQVR RCLINDLNPQ AVERAISRLR
160 170 180 190 200
ENREFVPLCV SALARSRADW LYGINMTRAY TLLGRNAGYD GVLSVGRVQT
210 220 230 240 250
PVLGLVVRRD EEIENFVPRD YFEVKAHIVT PAEERFVAMW QPSESCEPYQ
260 270 280 290 300
DEEGRLLHRP LAEHVARRIE GQPAQVIAYN DKRESETAPL PYSLSALQIE
310 320 330 340 350
AAKRYGLSAQ QVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRQAVMNA
360 370 380 390 400
IAAHRPDMLP QPAVDSERRN RCWDDSKVDA HHAIIPTARS ARVTLTESEN
410 420 430 440 450
QVYGLVARQY LMQFCADAVF RKCVIELEIA GGKFVAKARF LAEAGWRTLL
460 470 480 490 500
GGKERDEDNE GTPLPVVSKG DALLCERGEV VDRQTQPPRP FTDATLLSAM
510 520 530 540 550
TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRAF LFKKGRSIHA
560 570 580 590 600
TEAGRALIHA LPPSAAHPDM TAHWESTLTQ ISEKRCRYQD FMQPLTQSLY
610 620 630 640
SLIQQAQQTS NMSMFSGLPP TKRATAKRRK PSSRAKEQQS
Length:640
Mass (Da):72,252
Last modified:September 1, 2009 - v1
Checksum:i9311E80F23DF3527
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001654 Genomic DNA. Translation: ACS85756.1.

Genome annotation databases

EnsemblBacteriaiACS85756; ACS85756; Dd703_1966.
KEGGidda:Dd703_1966.
PATRICi21791356. VBIDicDad95084_2101.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001654 Genomic DNA. Translation: ACS85756.1.

3D structure databases

ProteinModelPortaliC6C5W5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi579405.Dd703_1966.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACS85756; ACS85756; Dd703_1966.
KEGGidda:Dd703_1966.
PATRICi21791356. VBIDicDad95084_2101.

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
KOiK03169.
OMAiSTYPDMT.
OrthoDBiEOG60CWM6.

Enzyme and pathway databases

BioCyciDDAD579405:GHJU-2007-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. 2 hits.
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: Ech703Imported.

Entry informationi

Entry nameiC6C5W5_DICDC
AccessioniPrimary (citable) accession number: C6C5W5
Entry historyi
Integrated into UniProtKB/TrEMBL: September 1, 2009
Last sequence update: September 1, 2009
Last modified: July 6, 2016
This is version 62 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.