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Protein

DNA topoisomerase 3

Gene

topB

Organism
Staphylococcus epidermidis (strain ATCC 12228)
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 annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi8Magnesium; catalyticUniRule annotation1
Metal bindingi104Magnesium; catalyticUniRule annotation1
Active sitei305O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

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:SE_1828
OrganismiStaphylococcus epidermidis (strain ATCC 12228)
Taxonomic identifieri176280 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus
Proteomesi
  • UP000001411 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002863771 – 711DNA topoisomerase 3Add BLAST711

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei60Interaction with DNAUniRule annotation1
Sitei167Interaction with DNAUniRule annotation1
Sitei175Interaction with DNAUniRule annotation1
Sitei307Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi176280.SE1828.

Structurei

3D structure databases

ProteinModelPortaliQ8CRF7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 135ToprimUniRule annotationAdd BLAST134

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni186 – 191Interaction with DNAUniRule annotation6

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi560 – 710Lys-richAdd BLAST151

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C9U. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
KOiK03169.
OMAiTKHDEYF.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00953. Topoisom_3_prok. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
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.

Q8CRF7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKSLILAEKP SVGRDIANAL NLQQKSNGYI EGKQYIVTWA LGHLVTNATP
60 70 80 90 100
EQYNPSYKEW NLEDLPIIPK KMKTVVISKT NRQFKIVKSL ILDKNVKEII
110 120 130 140 150
IATDAGREGE LVARLILDKV GNKKPIKRLW ISSVTKKAIQ EGFKQLKNGN
160 170 180 190 200
AYQNLYEAAL ARSEADWIVG INATRALTTK YDAQLSLGRV QTPTIQIVKS
210 220 230 240 250
RQDEINYFKP EKYYTLSINV DGYDLNLKQQ KRYKDKKELE LIEHKIKHQE
260 270 280 290 300
GKILEVKGKN KKSYAQPLFN LTDLQQEAYK RYKMGPKETL NTLQHLYERH
310 320 330 340 350
KLVTYPRTDS NYLTDDMVDT IQERLRAILA TDYKSHVRDL ISESFSSKMH
360 370 380 390 400
IFNNQKVSDH HAIIPTEVRP SIEQLSQREF KIYMLIAERF LENLMNPYLY
410 420 430 440 450
EVLTIHAQLK DYNFVLKEII PKQLGYKALK DQTSSHTLTH SFKEGQLFKV
460 470 480 490 500
HRIEIHEHET KAPEYFNEGS LLKAMENPQN HIDLNDKKYA KTLKHSGGIG
510 520 530 540 550
TVATRADIIE KLFNMNALES RDGKIKVTSK GKQILELSPS ELTSPILTAQ
560 570 580 590 600
WEEKLMLIEK GKYNSQKFIQ EMKNFTFKVV NKIKSSEQKY KHDNLTTTEC
610 620 630 640 650
PTCGKFMIKV KTKNGQMLVC QDPKCKTKKN IQRKTNARCP NCKKKMTLFG
660 670 680 690 700
KGKEAVYRCV CGHTETQSQM DKRMRDKTNG KVSRKEMKKY INKKEEIDNN
710
PFKDALKNLK L
Length:711
Mass (Da):82,363
Last modified:March 1, 2003 - v1
Checksum:i310843E31D80365C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE015929 Genomic DNA. Translation: AAO05469.1.
RefSeqiNP_765383.1. NC_004461.1.
WP_001829767.1. NC_004461.1.

Genome annotation databases

EnsemblBacteriaiAAO05469; AAO05469; SE_1828.
GeneIDi1057342.
KEGGisep:SE1828.
PATRICi19609528. VBIStaEpi113981_1784.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE015929 Genomic DNA. Translation: AAO05469.1.
RefSeqiNP_765383.1. NC_004461.1.
WP_001829767.1. NC_004461.1.

3D structure databases

ProteinModelPortaliQ8CRF7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi176280.SE1828.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO05469; AAO05469; SE_1828.
GeneIDi1057342.
KEGGisep:SE1828.
PATRICi19609528. VBIStaEpi113981_1784.

Phylogenomic databases

eggNOGiENOG4105C9U. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
KOiK03169.
OMAiTKHDEYF.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00953. Topoisom_3_prok. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
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...

Entry informationi

Entry nameiTOP3_STAES
AccessioniPrimary (citable) accession number: Q8CRF7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: March 1, 2003
Last modified: November 2, 2016
This is version 91 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

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.