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P40687

- TOP3_SALTY

UniProt

P40687 - TOP3_SALTY

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Protein

DNA topoisomerase 3

Gene

topB

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.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotationNote: Binds two Mg(2+) per subunit.UniRule annotation

Sites

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

GO - Molecular functioni

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

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 3UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IIIUniRule annotation
Gene namesi
Name:topBUniRule annotation
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 3PRO_0000145186Add
BLAST

Proteomic databases

PaxDbiP40687.
PRIDEiP40687.

Interactioni

Protein-protein interaction databases

STRINGi99287.STM1298.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LMUmodel-A1-649[»]
ProteinModelPortaliP40687.
SMRiP40687. Positions 1-623.
ModBaseiSearch...
MobiDBiSearch...

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 DNAUniRule annotation

Sequence similaritiesi

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

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_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.

P40687-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MRLFIAEKPS LGRAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ
60 70 80 90 100
PDAYDSRYAR WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHQAGEIIH
110 120 130 140 150
AGDPDREGQL LVDEVLDYLQ LPAEKRQQVR RCLINDLNPQ AVERAIDRLR
160 170 180 190 200
ANSDFVPLCV SALARARADW LYGINMTRAY TILGRNAGYQ GVLSVGRVQT
210 220 230 240 250
PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW QPSEACEPYQ
260 270 280 290 300
DEEGRLLHRP LAEHVVNRIN GQPALVTSYN DKRESESAPL PFSLSTLQIE
310 320 330 340 350
AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRQAVMNA
360 370 380 390 400
ISVHAPDLLP QPVVNPDTRN RCWDDKKVDA HHAIIPTARS SSVHLTENEA
410 420 430 440 450
KVYTLIARQY LMQFCPDAVF RKCVIELEIA KGKFVAKARF LAEAGWRTLL
460 470 480 490 500
GSKERDEEND GTPLPVVAKG DELLCEKGEV VERQTQPPRH FTDATLLSAM
510 520 530 540 550
TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRSF LTKKGRYIHS
560 570 580 590 600
TDAGKALIHS LPEMAARPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY
610 620 630 640
QLIEQAKRTP VKRFRGIVAP GGGDKKKSAP RKRAGKKSPP AAETGRQTE
Length:649
Mass (Da):73,039
Last modified:December 13, 2001 - v2
Checksum:iBF8212CEB33F4669
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1LMU model - A 1-649 [» ]
ProteinModelPortali P40687.
SMRi P40687. Positions 1-623.
ModBasei Search...
MobiDBi 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_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. 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: November 26, 2014
This is version 119 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