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P14294

- TOP3_ECOLI

UniProt

P14294 - TOP3_ECOLI

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Protein

DNA topoisomerase 3

Gene

topB

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.2 PublicationsUniRule annotation

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.1 PublicationUniRule annotation

Cofactori

Magnesium. 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+ and Ca2+.1 PublicationUniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Magnesium 1; catalyticUniRule annotation
Sitei61 – 611Interaction with DNA
Metal bindingi103 – 1031Magnesium 1; catalyticUniRule annotation
Metal bindingi103 – 1031Magnesium 2UniRule annotation
Metal bindingi105 – 1051Magnesium 2UniRule annotation
Sitei170 – 1701Interaction with DNA
Sitei178 – 1781Interaction with DNA
Sitei185 – 1851Interaction with DNA
Active sitei328 – 3281O-(5'-phospho-DNA)-tyrosine intermediate1 PublicationUniRule annotation
Sitei330 – 3301Interaction with DNA

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA topoisomerase type I activity Source: EcoliWiki
  3. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. chromosome separation Source: EcoliWiki
  2. DNA recombination Source: EcoliWiki
  3. DNA topological change Source: UniProtKB-HAMAP
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.

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11014. topB.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 653653DNA topoisomerase 3PRO_0000145184Add
BLAST

Proteomic databases

PaxDbiP14294.
PRIDEiP14294.

Expressioni

Gene expression databases

GenevestigatoriP14294.

Interactioni

Protein-protein interaction databases

DIPiDIP-11012N.
IntActiP14294. 39 interactions.
MINTiMINT-1224249.
STRINGi511145.b1763.

Structurei

Secondary structure

1
653
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87
Helixi9 – 168
Beta strandi24 – 263
Beta strandi29 – 324
Turni33 – 353
Beta strandi36 – 405
Beta strandi45 – 484
Helixi51 – 544
Helixi56 – 594
Helixi63 – 653
Beta strandi75 – 773
Helixi79 – 813
Helixi82 – 9413
Beta strandi96 – 1016
Helixi106 – 11813
Helixi123 – 1275
Beta strandi129 – 1313
Helixi139 – 1468
Helixi152 – 1554
Helixi156 – 18530
Turni186 – 1883
Helixi199 – 21416
Beta strandi220 – 22910
Beta strandi235 – 2406
Helixi244 – 2463
Turni247 – 2493
Beta strandi252 – 2543
Helixi259 – 26911
Beta strandi273 – 2753
Beta strandi278 – 2869
Helixi294 – 30512
Helixi309 – 32113
Helixi338 – 3436
Helixi344 – 35411
Turni356 – 3583
Beta strandi371 – 3733
Helixi375 – 3773
Helixi397 – 41216
Beta strandi418 – 42710
Beta strandi434 – 4363
Beta strandi438 – 4436
Helixi445 – 4495
Helixi454 – 4563
Beta strandi472 – 48413
Helixi493 – 5019
Helixi503 – 5064
Helixi510 – 5189
Beta strandi521 – 5233
Turni525 – 5273
Helixi528 – 53710
Beta strandi540 – 55011
Helixi552 – 5609
Helixi563 – 5664
Helixi569 – 58214
Helixi588 – 60720
Helixi612 – 6143
Helixi649 – 6535

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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. Positions 1-620.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14294.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 134134ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni194 – 1996Interaction with DNA

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0550.
HOGENOMiHOG000086848.
InParanoidiP14294.
KOiK03169.
OMAiSNRDFIP.
OrthoDBiEOG60CWM6.
PhylomeDBiP14294.

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. 1 hit.
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:
EMBL
GenBank
DDBJ
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.
YP_490024.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74833; AAC74833; b1763.
BAA15551; BAA15551; BAA15551.
GeneIDi12930143.
946141.
KEGGiecj:Y75_p1738.
eco:b1763.
PATRICi32118837. VBIEscCol129921_1836.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J05076 Genomic DNA. Translation: AAA83923.1 .
U00096 Genomic DNA. Translation: AAC74833.1 .
AP009048 Genomic DNA. Translation: BAA15551.1 .
PIRi JV0049.
RefSeqi NP_416277.1. NC_000913.3.
YP_490024.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1D6M X-ray 3.00 A 1-653 [» ]
1I7D X-ray 2.05 A 1-653 [» ]
2O19 X-ray 2.45 A/B 1-653 [» ]
2O54 X-ray 2.50 A/B 1-653 [» ]
2O59 X-ray 2.50 A/B 1-653 [» ]
2O5C X-ray 2.35 A/B 1-653 [» ]
2O5E X-ray 2.50 A/B 1-653 [» ]
ProteinModelPortali P14294.
SMRi P14294. Positions 1-620.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-11012N.
IntActi P14294. 39 interactions.
MINTi MINT-1224249.
STRINGi 511145.b1763.

Proteomic databases

PaxDbi P14294.
PRIDEi P14294.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74833 ; AAC74833 ; b1763 .
BAA15551 ; BAA15551 ; BAA15551 .
GeneIDi 12930143.
946141.
KEGGi ecj:Y75_p1738.
eco:b1763.
PATRICi 32118837. VBIEscCol129921_1836.

Organism-specific databases

EchoBASEi EB1007.
EcoGenei EG11014. topB.

Phylogenomic databases

eggNOGi COG0550.
HOGENOMi HOG000086848.
InParanoidi P14294.
KOi K03169.
OMAi SNRDFIP.
OrthoDBi EOG60CWM6.
PhylomeDBi P14294.

Enzyme and pathway databases

BioCyci EcoCyc:EG11014-MONOMER.
ECOL316407:JW1752-MONOMER.
MetaCyc:EG11014-MONOMER.

Miscellaneous databases

EvolutionaryTracei P14294.
PROi P14294.

Gene expression databases

Genevestigatori P14294.

Family and domain databases

Gene3Di 1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPi MF_00953. Topoisom_3_prok.
InterProi 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.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR005738. TopoIII.
IPR006171. Toprim_domain.
[Graphical view ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00417. PRTPISMRASEI.
SMARTi SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view ]
SUPFAMi SSF56712. SSF56712. 1 hit.
TIGRFAMsi TIGR01056. topB. 1 hit.
PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning and DNA sequence analysis of Escherichia coli topB, the gene encoding topoisomerase III."
    Digate R.J., Marians K.J.
    J. Biol. Chem. 264:17924-17930(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20, FUNCTION.
    Strain: HMS-83.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Escherichia coli DNA topoisomerase III: purification and characterization of a new type I enzyme."
    Srivenugopal K.S., Lockshon D., Morris D.R.
    Biochemistry 23:1899-1906(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION, COFACTOR.
  6. "The structure of Escherichia coli DNA topoisomerase III."
    Mondragon A., DiGate R.
    Structure 7:1373-1383(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS), ACTIVE SITE.
  7. "Crystal structure of a complex of a type IA DNA topoisomerase with a single-stranded DNA molecule."
    Changela A., DiGate R.J., Mondragon A.
    Nature 411:1077-1081(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF MUTANT PHE-328 IN COMPLEX WITH DNA.
  8. "Structural studies of E. coli topoisomerase III-DNA complexes reveal a novel type IA topoisomerase-DNA conformational intermediate."
    Changela A., DiGate R.J., Mondragon A.
    J. Mol. Biol. 368:105-118(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEXES WITH DNA.

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: October 29, 2014
This is version 138 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

External Data

Dasty 3