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Protein

DNA topoisomerase 3

Gene

topB

Organism
Dickeya paradisiaca (strain Ech703) (Dickeya dadantii (strain Ech703))
Status
Unreviewed-Annotation score: -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 bindingi7Magnesium 1; catalyticUniRule annotation1
Metal bindingi103Magnesium 1; catalyticUniRule annotation1
Metal bindingi103Magnesium 2UniRule annotation1
Metal bindingi105Magnesium 2UniRule annotation1
Active sitei328O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-bindingUniRule annotation, Isomerase, TopoisomeraseUniRule annotation
LigandMagnesiumUniRule annotation, Metal-bindingUniRule annotation

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 paradisiaca (strain Ech703) (Dickeya dadantii (strain Ech703))Imported
Taxonomic identifieri579405 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesPectobacteriaceaeDickeya
Proteomesi
  • UP000002734 Componenti: Chromosome

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei61Interaction with DNAUniRule annotation1
Sitei170Interaction with DNAUniRule annotation1
Sitei178Interaction with DNAUniRule annotation1
Sitei185Interaction with DNAUniRule annotation1
Sitei330Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi579405.Dd703_1966

Structurei

3D structure databases

ProteinModelPortaliC6C5W5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 134ToprimInterPro annotationAdd BLAST134

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni194 – 199Interaction with DNAUniRule annotation6

Sequence similaritiesi

Belongs to the type IA topoisomerase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C73 Bacteria
COG0550 LUCA
HOGENOMiHOG000086848
KOiK03169
OMAiTYPRVDT
OrthoDBiPOG091H028X

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03362 TOPRIM_TopoIA_TopoIII, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 2 hits
2.70.20.10, 2 hits
HAMAPiMF_00953 Topoisom_3_prok, 1 hit
InterProiView protein in InterPro
IPR000380 Topo_IA
IPR003601 Topo_IA_2
IPR023406 Topo_IA_AS
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
IPR005738 TopoIII
IPR006171 TOPRIM_domain
IPR034144 TOPRIM_TopoIII
PANTHERiPTHR11390 PTHR11390, 1 hit
PfamiView protein in Pfam
PF01131 Topoisom_bac, 1 hit
PF01751 Toprim, 1 hit
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SUPFAMiSSF56712 SSF56712, 1 hit
TIGRFAMsiTIGR01056 topB, 1 hit
PROSITEiView protein in PROSITE
PS00396 TOPOISOMERASE_I_PROK, 1 hit
PS50880 TOPRIM, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

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

Similar proteinsi

Entry informationi

Entry nameiC6C5W5_DICP7
AccessioniPrimary (citable) accession number: C6C5W5
Entry historyiIntegrated into UniProtKB/TrEMBL: September 1, 2009
Last sequence update: September 1, 2009
Last modified: April 25, 2018
This is version 73 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported
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Main funding by: National Institutes of Health