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Protein

DNA topoisomerase 3

Gene

topB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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. TOP3 is a potent decatenase.UniRule annotation2 Publications

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotation1 Publication

Cofactori

Mg2+UniRule annotation1 Publication, Mn2+UniRule annotation1 Publication, Ca2+UniRule annotation1 PublicationNote: Binds two Mg2+ ions per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ or Ca2+.UniRule annotation1 Publication

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 Publication1

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • DNA topoisomerase type I activity Source: EcoliWiki
  • magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • chromosome separation Source: EcoliWiki
  • DNA recombination Source: EcoliWiki
  • DNA topological change Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11014-MONOMER.
ECOL316407:JW1752-MONOMER.
MetaCyc:EG11014-MONOMER.
BRENDAi5.99.1.2. 2026.

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:b1763, JW1752
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11014. topB.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451841 – 653DNA topoisomerase 3Add BLAST653

Proteomic databases

PaxDbiP14294.
PRIDEiP14294.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei61Interaction with DNA1
Sitei170Interaction with DNA1
Sitei178Interaction with DNA1
Sitei185Interaction with DNA1
Sitei330Interaction with DNA1

Protein-protein interaction databases

BioGridi4259137. 56 interactors.
DIPiDIP-11012N.
IntActiP14294. 39 interactors.
MINTiMINT-1224249.
STRINGi511145.b1763.

Structurei

Secondary structure

1653
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 8Combined sources7
Helixi9 – 16Combined sources8
Beta strandi24 – 26Combined sources3
Beta strandi29 – 32Combined sources4
Turni33 – 35Combined sources3
Beta strandi36 – 40Combined sources5
Beta strandi45 – 48Combined sources4
Helixi51 – 54Combined sources4
Helixi56 – 59Combined sources4
Helixi63 – 65Combined sources3
Beta strandi75 – 77Combined sources3
Helixi79 – 81Combined sources3
Helixi82 – 94Combined sources13
Beta strandi96 – 101Combined sources6
Helixi106 – 118Combined sources13
Helixi123 – 127Combined sources5
Beta strandi129 – 131Combined sources3
Helixi139 – 146Combined sources8
Helixi152 – 155Combined sources4
Helixi156 – 185Combined sources30
Turni186 – 188Combined sources3
Helixi199 – 214Combined sources16
Beta strandi220 – 229Combined sources10
Beta strandi235 – 240Combined sources6
Helixi244 – 246Combined sources3
Turni247 – 249Combined sources3
Beta strandi252 – 254Combined sources3
Helixi259 – 269Combined sources11
Beta strandi273 – 275Combined sources3
Beta strandi278 – 286Combined sources9
Helixi294 – 305Combined sources12
Helixi309 – 321Combined sources13
Helixi338 – 343Combined sources6
Helixi344 – 354Combined sources11
Turni356 – 358Combined sources3
Beta strandi371 – 373Combined sources3
Helixi375 – 377Combined sources3
Helixi397 – 412Combined sources16
Beta strandi418 – 427Combined sources10
Beta strandi434 – 436Combined sources3
Beta strandi438 – 443Combined sources6
Helixi445 – 449Combined sources5
Helixi454 – 456Combined sources3
Beta strandi472 – 484Combined sources13
Helixi493 – 501Combined sources9
Helixi503 – 506Combined sources4
Helixi510 – 518Combined sources9
Beta strandi521 – 523Combined sources3
Turni525 – 527Combined sources3
Helixi528 – 537Combined sources10
Beta strandi540 – 550Combined sources11
Helixi552 – 560Combined sources9
Helixi563 – 566Combined sources4
Helixi569 – 582Combined sources14
Helixi588 – 607Combined sources20
Helixi612 – 614Combined sources3
Helixi649 – 653Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1D6MX-ray3.00A1-653[»]
1I7DX-ray2.05A1-653[»]
2O19X-ray2.45A/B1-653[»]
2O54X-ray2.50A/B1-653[»]
2O59X-ray2.50A/B1-653[»]
2O5CX-ray2.35A/B1-653[»]
2O5EX-ray2.50A/B1-653[»]
ProteinModelPortaliP14294.
SMRiP14294.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14294.

Family & Domainsi

Domains and Repeats

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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni194 – 199Interaction with DNA6

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
InParanoidiP14294.
KOiK03169.
OMAiRRFRGIV.
PhylomeDBiP14294.

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.

P14294-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLFIAEKPS LARAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ
60 70 80 90 100
PDAYDSRYAR WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHEASEIVH
110 120 130 140 150
AGDPDREGQL LVDEVLDYLQ LAPEKRQQVQ RCLINDLNPQ AVERAIDRLR
160 170 180 190 200
SNSEFVPLCV SALARARADW LYGINMTRAY TILGRNAGYQ GVLSVGRVQT
210 220 230 240 250
PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW QPSEACEPYQ
260 270 280 290 300
DEEGRLLHRP LAEHVVNRIS GQPAIVTSYN DKRESESAPL PFSLSALQIE
310 320 330 340 350
AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRHAVMNA
360 370 380 390 400
ISVHAPDLLP QPVVDPDIRN RCWDDKKVDA HHAIIPTARS SAINLTENEA
410 420 430 440 450
KVYNLIARQY LMQFCPDAVF RKCVIELDIA KGKFVAKARF LAEAGWRTLL
460 470 480 490 500
GSKERDEEND GTPLPVVAKG DELLCEKGEV VERQTQPPRH FTDATLLSAM
510 520 530 540 550
TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRGF LTKKGRYIHS
560 570 580 590 600
TDAGKALFHS LPEMATRPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY
610 620 630 640 650
QLIDQAKRTP VRQFRGIVAP GSGGSADKKK AAPRKRSAKK SPPADEVGSG

AIA
Length:653
Mass (Da):73,217
Last modified:January 1, 1990 - v1
Checksum:i301566E14DDDD8C7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05076 Genomic DNA. Translation: AAA83923.1.
U00096 Genomic DNA. Translation: AAC74833.1.
AP009048 Genomic DNA. Translation: BAA15551.1.
PIRiJV0049.
RefSeqiNP_416277.1. NC_000913.3.
WP_001235800.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74833; AAC74833; b1763.
BAA15551; BAA15551; BAA15551.
GeneIDi946141.
KEGGiecj:JW1752.
eco:b1763.
PATRICi32118837. VBIEscCol129921_1836.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05076 Genomic DNA. Translation: AAA83923.1.
U00096 Genomic DNA. Translation: AAC74833.1.
AP009048 Genomic DNA. Translation: BAA15551.1.
PIRiJV0049.
RefSeqiNP_416277.1. NC_000913.3.
WP_001235800.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1D6MX-ray3.00A1-653[»]
1I7DX-ray2.05A1-653[»]
2O19X-ray2.45A/B1-653[»]
2O54X-ray2.50A/B1-653[»]
2O59X-ray2.50A/B1-653[»]
2O5CX-ray2.35A/B1-653[»]
2O5EX-ray2.50A/B1-653[»]
ProteinModelPortaliP14294.
SMRiP14294.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259137. 56 interactors.
DIPiDIP-11012N.
IntActiP14294. 39 interactors.
MINTiMINT-1224249.
STRINGi511145.b1763.

Proteomic databases

PaxDbiP14294.
PRIDEiP14294.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74833; AAC74833; b1763.
BAA15551; BAA15551; BAA15551.
GeneIDi946141.
KEGGiecj:JW1752.
eco:b1763.
PATRICi32118837. VBIEscCol129921_1836.

Organism-specific databases

EchoBASEiEB1007.
EcoGeneiEG11014. topB.

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
HOGENOMiHOG000086848.
InParanoidiP14294.
KOiK03169.
OMAiRRFRGIV.
PhylomeDBiP14294.

Enzyme and pathway databases

BioCyciEcoCyc:EG11014-MONOMER.
ECOL316407:JW1752-MONOMER.
MetaCyc:EG11014-MONOMER.
BRENDAi5.99.1.2. 2026.

Miscellaneous databases

EvolutionaryTraceiP14294.
PROiP14294.

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_ECOLI
AccessioniPrimary (citable) accession number: P14294
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: November 2, 2016
This is version 152 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.