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P40687

- TOP3_SALTY

UniProt

P40687 - TOP3_SALTY

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Protein
DNA topoisomerase 3
Gene
topB, STM1298
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - 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 By similarity.UniRule annotation

Catalytic activityi

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

Cofactori

Magnesium. Binds two Mg2+ per subunit By similarity.UniRule annotation

Sites

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

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: UniProtKB-KW
  3. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP
Complete GO annotation...

GO - Biological processi

  1. 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

BioCyciSENT99287:GCTI-1309-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 3 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase III
Gene namesi
Name:topB
Ordered Locus Names:STM1298
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 649649DNA topoisomerase 3UniRule annotation
PRO_0000145186Add
BLAST

Proteomic databases

PaxDbiP40687.
PRIDEiP40687.

Interactioni

Protein-protein interaction databases

STRINGi99287.STM1298.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87
Helixi9 – 1810
Beta strandi27 – 326
Turni33 – 353
Beta strandi36 – 405
Beta strandi45 – 484
Helixi51 – 544
Helixi56 – 594
Beta strandi75 – 773
Turni79 – 813
Helixi82 – 9413
Beta strandi96 – 1016
Helixi106 – 11813
Helixi123 – 1286
Helixi139 – 1479
Helixi152 – 1554
Helixi156 – 18732
Helixi199 – 21416
Beta strandi220 – 22910
Beta strandi235 – 2406
Helixi244 – 2496
Helixi259 – 26911
Beta strandi273 – 28614
Helixi294 – 30512
Helixi309 – 32113
Helixi338 – 3436
Helixi344 – 35411
Turni356 – 3583
Helixi397 – 41216
Beta strandi418 – 43114
Beta strandi433 – 44311
Helixi445 – 4495
Helixi452 – 4565
Beta strandi472 – 48413
Helixi493 – 5019
Helixi503 – 5064
Helixi510 – 5189
Helixi527 – 53711
Beta strandi540 – 5445
Beta strandi547 – 5504
Helixi552 – 5609
Helixi563 – 5664
Helixi569 – 58214
Helixi588 – 60821
Helixi612 – 6143

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LMUmodel-A1-649[»]
ProteinModelPortaliP40687.
SMRiP40687. Positions 1-623.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 134134Toprim
Add
BLAST

Region

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

Sequence similaritiesi

Contains 1 Toprim domain.

Phylogenomic databases

eggNOGiCOG0550.
HOGENOMiHOG000086848.
KOiK03169.
OMAiMANPDAY.
OrthoDBiEOG60CWM6.
PhylomeDBiP40687.

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.
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.

P40687-1 [UniParc]FASTAAdd to Basket

« Hide

MRLFIAEKPS LGRAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ    50
PDAYDSRYAR WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHQAGEIIH 100
AGDPDREGQL LVDEVLDYLQ LPAEKRQQVR RCLINDLNPQ AVERAIDRLR 150
ANSDFVPLCV SALARARADW LYGINMTRAY TILGRNAGYQ GVLSVGRVQT 200
PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW QPSEACEPYQ 250
DEEGRLLHRP LAEHVVNRIN GQPALVTSYN DKRESESAPL PFSLSTLQIE 300
AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRQAVMNA 350
ISVHAPDLLP QPVVNPDTRN RCWDDKKVDA HHAIIPTARS SSVHLTENEA 400
KVYTLIARQY LMQFCPDAVF RKCVIELEIA KGKFVAKARF LAEAGWRTLL 450
GSKERDEEND GTPLPVVAKG DELLCEKGEV VERQTQPPRH FTDATLLSAM 500
TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRSF LTKKGRYIHS 550
TDAGKALIHS LPEMAARPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY 600
QLIEQAKRTP VKRFRGIVAP GGGDKKKSAP RKRAGKKSPP AAETGRQTE 649
Length:649
Mass (Da):73,039
Last modified:December 13, 2001 - v2
Checksum:iBF8212CEB33F4669
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE006468 Genomic DNA. Translation: AAL20223.1.
M24021 Genomic DNA. No translation available.
RefSeqiNP_460264.1. NC_003197.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE006468 Genomic DNA. Translation: AAL20223.1 .
M24021 Genomic DNA. No translation available.
RefSeqi NP_460264.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1LMU model - A 1-649 [» ]
ProteinModelPortali P40687.
SMRi P40687. Positions 1-623.
ModBasei Search...

Protein-protein interaction databases

STRINGi 99287.STM1298.

Proteomic databases

PaxDbi P40687.
PRIDEi P40687.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL20223 ; AAL20223 ; STM1298 .
GeneIDi 1252816.
KEGGi stm:STM1298.
PATRICi 32381073. VBISalEnt20916_1379.

Phylogenomic databases

eggNOGi COG0550.
HOGENOMi HOG000086848.
KOi K03169.
OMAi MANPDAY.
OrthoDBi EOG60CWM6.
PhylomeDBi P40687.

Enzyme and pathway databases

BioCyci SENT99287:GCTI-1309-MONOMER.

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.
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. 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.

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: September 3, 2014
This is version 116 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

External Data

Dasty 3

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