Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P40687

- TOP3_SALTY

UniProt

P40687 - TOP3_SALTY

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
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 2 (13 Dec 2001)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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

    Magnesium. Binds two Mg2+ 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

    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

    Secondary structure

    1
    649
    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.
    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.
    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...
    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.
    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

    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: October 1, 2014
    This is version 117 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