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Protein

DNA topoisomerase 3

Gene

topB

Organism
Haemophilus parasuis serovar 5 (strain SH0165)
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 sitei329 – 3291O-(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

BioCyciHPAR557723:GH24-428-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 annotationImported
Ordered Locus Names:HAPS_0428Imported
OrganismiHaemophilus parasuis serovar 5 (strain SH0165)Imported
Taxonomic identifieri557723 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
Proteomesi
  • UP000006743 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
Sitei331 – 3311Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi557723.HAPS_0428.

Structurei

3D structure databases

ProteinModelPortaliB8F447.
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

eggNOGiENOG4108IYH. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
KOiK03169.
OMAiRKVGYQG.
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.

B8F447-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLFIAEKPS LGRAIADVLP KPHTRGDGFI QCGEDNVVTW CIGHLLEQAE
60 70 80 90 100
PDAYDERFKM WRMEHLPIIP EQWKLIPKKE TLKQFKVVER LIKQADILVN
110 120 130 140 150
AGDPDREGQL LVDEVFGYLN LSPERKSQIQ RCLISDLNPN AVKKAIEKLQ
160 170 180 190 200
FNRDFVPLAT SALARARADW LYGINMTRAY TLQGRWAGYK GVLSVGRVQT
210 220 230 240 250
PVLGLIVRRD LEIENFIPKD YFEVLANVVV PETQERFQAQ WQPSKACEDY
260 270 280 290 300
QDEDGRVLSR PLAENVVKRI TDQAACVTEY QDKMESEAAP LPYSLSALQI
310 320 330 340 350
DAARRFGLSA QDVLDVCQRL YETHKLITYP RSDNRYLPNE HFADRLKVMA
360 370 380 390 400
AIAHHLPEYA QKPDAVDPNK KNRCWNDSKV EAHHAIIPTA RQGRQVHLTQ
410 420 430 440 450
NEQWIYQLIA RQYLMQFCPD AEYRKGKIVL NIAGGTFIAQ ARNLVVAGWK
460 470 480 490 500
SLLGKEDNDE IVEPLLPVVK KDQQLWCESG EIISKKTQPP RHFTDATLLS
510 520 530 540 550
AMTGIARFVQ DKQLKKVLRE TDGLGTEATR AGIIELLFKR GFLIKKGRNI
560 570 580 590 600
HSTEAGRTLI SALPDVATQP DMTAHWEMQL TDISKKQASY QQFMADLNQR
610 620 630 640
LPSLLSSPNK QILQSLAKIT PLTTSSKSRY TRKSTQNVEK
Length:640
Mass (Da):72,886
Last modified:March 3, 2009 - v1
Checksum:i9DE8AF6F5F744D26
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001321 Genomic DNA. Translation: ACL32099.1.
RefSeqiWP_012621725.1. NC_011852.1.

Genome annotation databases

EnsemblBacteriaiACL32099; ACL32099; HAPS_0428.
GeneIDi7276987.
KEGGihap:HAPS_0428.
PATRICi20193127. VBIHaePar127548_0432.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001321 Genomic DNA. Translation: ACL32099.1.
RefSeqiWP_012621725.1. NC_011852.1.

3D structure databases

ProteinModelPortaliB8F447.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi557723.HAPS_0428.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL32099; ACL32099; HAPS_0428.
GeneIDi7276987.
KEGGihap:HAPS_0428.
PATRICi20193127. VBIHaePar127548_0432.

Phylogenomic databases

eggNOGiENOG4108IYH. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
KOiK03169.
OMAiRKVGYQG.
OrthoDBiEOG60CWM6.

Enzyme and pathway databases

BioCyciHPAR557723:GH24-428-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. "Complete genome sequence of Haemophilus parasuis SH0165."
    Yue M., Yang F., Yang J., Bei W., Cai X., Chen L., Dong J., Zhou R., Jin M., Jin Q., Chen H.
    J. Bacteriol. 191:1359-1360(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SH0165Imported.

Entry informationi

Entry nameiB8F447_HAEPS
AccessioniPrimary (citable) accession number: B8F447
Entry historyi
Integrated into UniProtKB/TrEMBL: March 3, 2009
Last sequence update: March 3, 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 proteome, Reference 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.