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P40687 (TOP3_SALTY) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | 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

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:STM1298
OrganismSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]
Taxonomic identifier99287 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella

Protein attributes

Sequence length649 AA.
Sequence statusComplete.
Protein existenceInferred from homology

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 By similarity. HAMAP-Rule MF_00953

Catalytic activity

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. HAMAP-Rule MF_00953

Cofactor

Magnesium. Binds two Mg2+ per subunit By similarity. HAMAP-Rule MF_00953

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 – 649649DNA topoisomerase 3 HAMAP-Rule MF_00953
PRO_0000145186

Regions

Domain1 – 134134Toprim
Region194 – 1996Interaction with DNA By similarity

Sites

Active site3281O-(5'-phospho-DNA)-tyrosine intermediate By similarity
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 By similarity
Site1701Interaction with DNA By similarity
Site1781Interaction with DNA By similarity
Site1851Interaction with DNA By similarity
Site3301Interaction with DNA By similarity

Secondary structure

..................................................................................... 649
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P40687 [UniParc].

Last modified December 13, 2001. Version 2.
Checksum: BF8212CEB33F4669

FASTA64973,039
        10         20         30         40         50         60 
MRLFIAEKPS LGRAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ PDAYDSRYAR 

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

       130        140        150        160        170        180 
LPAEKRQQVR RCLINDLNPQ AVERAIDRLR ANSDFVPLCV SALARARADW LYGINMTRAY 

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

       250        260        270        280        290        300 
QPSEACEPYQ DEEGRLLHRP LAEHVVNRIN GQPALVTSYN DKRESESAPL PFSLSTLQIE 

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

       370        380        390        400        410        420 
QPVVNPDTRN RCWDDKKVDA HHAIIPTARS SSVHLTENEA KVYTLIARQY LMQFCPDAVF 

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

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

       550        560        570        580        590        600 
LTKKGRYIHS TDAGKALIHS LPEMAARPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY 

       610        620        630        640 
QLIEQAKRTP VKRFRGIVAP GGGDKKKSAP RKRAGKKSPP AAETGRQTE 

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2."
McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. expand/collapse author list , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K.
Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: LT2 / SGSC1412 / ATCC 700720.
[2]"Affinity labeling of a glutamyl peptide in the coenzyme binding site of NADP+-specific glutamate dehydrogenase of Salmonella typhimurium by 2-[(4-bromo-2,3-dioxobutyl)thio]-1,N6-ethenoadenosine 2',5'-bisphosphate."
Bansal A., Dayton M.A., Zalkin H., Colman R.F.
J. Biol. Chem. 264:9827-9835(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 601-649.
[3]"Large scale bacterial gene discovery by similarity search."
Robison K., Gilbert W., Church G.M.
Nat. Genet. 7:205-214(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE006468 Genomic DNA. Translation: AAL20223.1.
M24021 Genomic DNA. No translation available.
RefSeqNP_460264.1. NC_003197.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1LMUmodel-A1-649[»]
ProteinModelPortalP40687.
SMRP40687. Positions 1-623.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING99287.STM1298.

Proteomic databases

PaxDbP40687.
PRIDEP40687.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL20223; AAL20223; STM1298.
GeneID1252816.
KEGGstm:STM1298.
PATRIC32381073. VBISalEnt20916_1379.

Phylogenomic databases

eggNOGCOG0550.
HOGENOMHOG000086848.
KOK03169.
OMAMANPDAY.
OrthoDBEOG60CWM6.
PhylomeDBP40687.

Enzyme and pathway databases

BioCycSENT99287:GCTI-1309-MONOMER.

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.
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. SSF56712. 1 hit.
TIGRFAMsTIGR01056. topB. 1 hit.
PROSITEPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameTOP3_SALTY
AccessionPrimary (citable) accession number: P40687
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: December 13, 2001
Last modified: July 9, 2014
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references