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Protein

DNA topoisomerase 3

Gene

topB

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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)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

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:STM1298
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451861 – 649DNA topoisomerase 3Add BLAST649

Proteomic databases

PaxDbiP40687.

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

STRINGi99287.STM1298.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LMUmodel-A1-649[»]
ProteinModelPortaliP40687.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Region

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

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4108IYH. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
KOiK03169.
OMAiTQKKCPE.
PhylomeDBiP40687.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 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.
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.

P40687-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLFIAEKPS LGRAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ
60 70 80 90 100
PDAYDSRYAR WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHQAGEIIH
110 120 130 140 150
AGDPDREGQL LVDEVLDYLQ LPAEKRQQVR RCLINDLNPQ AVERAIDRLR
160 170 180 190 200
ANSDFVPLCV SALARARADW LYGINMTRAY TILGRNAGYQ GVLSVGRVQT
210 220 230 240 250
PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW QPSEACEPYQ
260 270 280 290 300
DEEGRLLHRP LAEHVVNRIN GQPALVTSYN DKRESESAPL PFSLSTLQIE
310 320 330 340 350
AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRQAVMNA
360 370 380 390 400
ISVHAPDLLP QPVVNPDTRN RCWDDKKVDA HHAIIPTARS SSVHLTENEA
410 420 430 440 450
KVYTLIARQY LMQFCPDAVF RKCVIELEIA KGKFVAKARF LAEAGWRTLL
460 470 480 490 500
GSKERDEEND GTPLPVVAKG DELLCEKGEV VERQTQPPRH FTDATLLSAM
510 520 530 540 550
TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRSF LTKKGRYIHS
560 570 580 590 600
TDAGKALIHS LPEMAARPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY
610 620 630 640
QLIEQAKRTP VKRFRGIVAP GGGDKKKSAP RKRAGKKSPP AAETGRQTE
Length:649
Mass (Da):73,039
Last modified:December 13, 2001 - v2
Checksum:iBF8212CEB33F4669
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL20223.1.
M24021 Genomic DNA. No translation available.
RefSeqiNP_460264.1. NC_003197.1.
WP_001235865.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL20223; AAL20223; STM1298.
GeneIDi1252816.
KEGGistm:STM1298.
PATRICi32381073. VBISalEnt20916_1379.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE006468 Genomic DNA. Translation: AAL20223.1.
M24021 Genomic DNA. No translation available.
RefSeqiNP_460264.1. NC_003197.1.
WP_001235865.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LMUmodel-A1-649[»]
ProteinModelPortaliP40687.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM1298.

Proteomic databases

PaxDbiP40687.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL20223; AAL20223; STM1298.
GeneIDi1252816.
KEGGistm:STM1298.
PATRICi32381073. VBISalEnt20916_1379.

Phylogenomic databases

eggNOGiENOG4108IYH. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
KOiK03169.
OMAiTQKKCPE.
PhylomeDBiP40687.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 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.
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...

Entry informationi

Entry nameiTOP3_SALTY
AccessioniPrimary (citable) accession number: P40687
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: December 13, 2001
Last modified: November 2, 2016
This is version 129 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.