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P14294 (TOP3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 126. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA topoisomerase 3
EC=5.99.1.2
Alternative name(s):
DNA topoisomerase III
Gene names
Name:topB
Ordered Locus Names:b1763, JW1752
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length653 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.5

Catalytic activity

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. Ref.5

Cofactor

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+. Ref.5

Sequence similarities

Belongs to the type IA topoisomerase family.

Contains 1 Toprim domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 653653DNA topoisomerase 3 HAMAP-Rule MF_00953
PRO_0000145184

Regions

Domain1 – 134134Toprim
Region194 – 1996Interaction with DNA HAMAP-Rule MF_00953

Sites

Active site3281O-(5'-phospho-DNA)-tyrosine intermediate Ref.6
Metal binding71Magnesium 1; catalytic By similarity
Metal binding1031Magnesium 1; catalytic By similarity
Metal binding1031Magnesium 2 By similarity
Metal binding1051Magnesium 2 By similarity
Site611Interaction with DNA
Site1701Interaction with DNA
Site1781Interaction with DNA
Site1851Interaction with DNA
Site3301Interaction with DNA

Secondary structure

1 ......................................................................................................... 653
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P14294 [UniParc].

Last modified January 1, 1990. Version 1.
Checksum: 301566E14DDDD8C7

FASTA65373,217
        10         20         30         40         50         60 
MRLFIAEKPS LARAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ PDAYDSRYAR 

        70         80         90        100        110        120 
WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHEASEIVH AGDPDREGQL LVDEVLDYLQ 

       130        140        150        160        170        180 
LAPEKRQQVQ RCLINDLNPQ AVERAIDRLR SNSEFVPLCV SALARARADW LYGINMTRAY 

       190        200        210        220        230        240 
TILGRNAGYQ GVLSVGRVQT PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW 

       250        260        270        280        290        300 
QPSEACEPYQ DEEGRLLHRP LAEHVVNRIS GQPAIVTSYN DKRESESAPL PFSLSALQIE 

       310        320        330        340        350        360 
AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRHAVMNA ISVHAPDLLP 

       370        380        390        400        410        420 
QPVVDPDIRN RCWDDKKVDA HHAIIPTARS SAINLTENEA KVYNLIARQY LMQFCPDAVF 

       430        440        450        460        470        480 
RKCVIELDIA KGKFVAKARF LAEAGWRTLL GSKERDEEND GTPLPVVAKG DELLCEKGEV 

       490        500        510        520        530        540 
VERQTQPPRH FTDATLLSAM TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRGF 

       550        560        570        580        590        600 
LTKKGRYIHS TDAGKALFHS LPEMATRPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY 

       610        620        630        640        650 
QLIDQAKRTP VRQFRGIVAP GSGGSADKKK AAPRKRSAKK SPPADEVGSG AIA

« Hide

References

« Hide 'large scale' references
[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]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		J05076 Genomic DNA. Translation: AAA83923.1.
U00096 Genomic DNA. Translation: AAC74833.1.
AP009048 Genomic DNA. Translation: BAA15551.1.
PIRJV0049.
RefSeqNP_416277.1. NC_000913.2.
YP_490024.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP14294.
SMRP14294. Positions 1-620.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-11012N.
IntActP14294. 39 interactions.
MINTMINT-1224249.
STRING511145.b1763.

Proteomic databases

PaxDbP14294.
PRIDEP14294.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74833; AAC74833; b1763.
BAA15551; BAA15551; BAA15551.
GeneID12930143.
946141.
KEGGecj:Y75_p1738.
eco:b1763.
PATRIC32118837. VBIEscCol129921_1836.

Organism-specific databases

EchoBASEEB1007.
EcoGeneEG11014. topB.

Phylogenomic databases

eggNOGCOG0550.
HOGENOMHOG000086848.
KOK03169.
OMAGNKERDE.
ProtClustDBPRK07726.

Enzyme and pathway databases

BioCycEcoCyc:EG11014-MONOMER.
ECOL316407:JW1752-MONOMER.
MetaCyc:EG11014-MONOMER.

Gene expression databases

GenevestigatorP14294.

Family and domain databases

Gene3D1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPMF_00953. Topoisom_3_prok.
InterProIPR000380. 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.
IPR005738. TopoIII_bac.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERPTHR11390. PTHR11390. 1 hit.
PfamPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSPR00417. PRTPISMRASEI.
SMARTSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMSSF56712. Topo_IA_core. 1 hit.
TIGRFAMsTIGR01056. topB. 1 hit.
PROSITEPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP14294.

Entry information

Entry nameTOP3_ECOLI
AccessionPrimary (citable) accession number: P14294
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: May 29, 2013
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents