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P14294

- TOP3_ECOLI

UniProt

P14294 - TOP3_ECOLI

Protein

DNA topoisomerase 3

Gene

topB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 137 (01 Oct 2014)
      Sequence version 1 (01 Jan 1990)
      Previous versions | rss
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    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. TOP3 is a potent decatenase.2 PublicationsUniRule annotation

    Catalytic activityi

    ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.1 PublicationUniRule annotation

    Cofactori

    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+.1 PublicationUniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi7 – 71Magnesium 1; catalyticUniRule annotation
    Sitei61 – 611Interaction with DNA
    Metal bindingi103 – 1031Magnesium 1; catalyticUniRule annotation
    Metal bindingi103 – 1031Magnesium 2UniRule annotation
    Metal bindingi105 – 1051Magnesium 2UniRule annotation
    Sitei170 – 1701Interaction with DNA
    Sitei178 – 1781Interaction with DNA
    Sitei185 – 1851Interaction with DNA
    Active sitei328 – 3281O-(5'-phospho-DNA)-tyrosine intermediate1 PublicationUniRule annotation
    Sitei330 – 3301Interaction with DNA

    GO - Molecular functioni

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

    GO - Biological processi

    1. chromosome separation Source: EcoliWiki
    2. DNA recombination Source: EcoliWiki
    3. DNA topological change Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11014-MONOMER.
    ECOL316407:JW1752-MONOMER.
    MetaCyc:EG11014-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:b1763, JW1752
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11014. topB.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 653653DNA topoisomerase 3PRO_0000145184Add
    BLAST

    Proteomic databases

    PaxDbiP14294.
    PRIDEiP14294.

    Expressioni

    Gene expression databases

    GenevestigatoriP14294.

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-11012N.
    IntActiP14294. 39 interactions.
    MINTiMINT-1224249.
    STRINGi511145.b1763.

    Structurei

    Secondary structure

    1
    653
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 87
    Helixi9 – 168
    Beta strandi24 – 263
    Beta strandi29 – 324
    Turni33 – 353
    Beta strandi36 – 405
    Beta strandi45 – 484
    Helixi51 – 544
    Helixi56 – 594
    Helixi63 – 653
    Beta strandi75 – 773
    Helixi79 – 813
    Helixi82 – 9413
    Beta strandi96 – 1016
    Helixi106 – 11813
    Helixi123 – 1275
    Beta strandi129 – 1313
    Helixi139 – 1468
    Helixi152 – 1554
    Helixi156 – 18530
    Turni186 – 1883
    Helixi199 – 21416
    Beta strandi220 – 22910
    Beta strandi235 – 2406
    Helixi244 – 2463
    Turni247 – 2493
    Beta strandi252 – 2543
    Helixi259 – 26911
    Beta strandi273 – 2753
    Beta strandi278 – 2869
    Helixi294 – 30512
    Helixi309 – 32113
    Helixi338 – 3436
    Helixi344 – 35411
    Turni356 – 3583
    Beta strandi371 – 3733
    Helixi375 – 3773
    Helixi397 – 41216
    Beta strandi418 – 42710
    Beta strandi434 – 4363
    Beta strandi438 – 4436
    Helixi445 – 4495
    Helixi454 – 4563
    Beta strandi472 – 48413
    Helixi493 – 5019
    Helixi503 – 5064
    Helixi510 – 5189
    Beta strandi521 – 5233
    Turni525 – 5273
    Helixi528 – 53710
    Beta strandi540 – 55011
    Helixi552 – 5609
    Helixi563 – 5664
    Helixi569 – 58214
    Helixi588 – 60720
    Helixi612 – 6143
    Helixi649 – 6535

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    ProteinModelPortaliP14294.
    SMRiP14294. Positions 1-620.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP14294.

    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 DNA

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0550.
    HOGENOMiHOG000086848.
    KOiK03169.
    OMAiSNRDFIP.
    OrthoDBiEOG60CWM6.
    PhylomeDBiP14294.

    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.

    P14294-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRLFIAEKPS LARAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ    50
    PDAYDSRYAR WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHEASEIVH 100
    AGDPDREGQL LVDEVLDYLQ LAPEKRQQVQ RCLINDLNPQ AVERAIDRLR 150
    SNSEFVPLCV SALARARADW LYGINMTRAY TILGRNAGYQ GVLSVGRVQT 200
    PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW QPSEACEPYQ 250
    DEEGRLLHRP LAEHVVNRIS GQPAIVTSYN DKRESESAPL PFSLSALQIE 300
    AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRHAVMNA 350
    ISVHAPDLLP QPVVDPDIRN RCWDDKKVDA HHAIIPTARS SAINLTENEA 400
    KVYNLIARQY LMQFCPDAVF RKCVIELDIA KGKFVAKARF LAEAGWRTLL 450
    GSKERDEEND GTPLPVVAKG DELLCEKGEV VERQTQPPRH FTDATLLSAM 500
    TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRGF LTKKGRYIHS 550
    TDAGKALFHS LPEMATRPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY 600
    QLIDQAKRTP VRQFRGIVAP GSGGSADKKK AAPRKRSAKK SPPADEVGSG 650
    AIA 653
    Length:653
    Mass (Da):73,217
    Last modified:January 1, 1990 - v1
    Checksum:i301566E14DDDD8C7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05076 Genomic DNA. Translation: AAA83923.1.
    U00096 Genomic DNA. Translation: AAC74833.1.
    AP009048 Genomic DNA. Translation: BAA15551.1.
    PIRiJV0049.
    RefSeqiNP_416277.1. NC_000913.3.
    YP_490024.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74833; AAC74833; b1763.
    BAA15551; BAA15551; BAA15551.
    GeneIDi12930143.
    946141.
    KEGGiecj:Y75_p1738.
    eco:b1763.
    PATRICi32118837. VBIEscCol129921_1836.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J05076 Genomic DNA. Translation: AAA83923.1 .
    U00096 Genomic DNA. Translation: AAC74833.1 .
    AP009048 Genomic DNA. Translation: BAA15551.1 .
    PIRi JV0049.
    RefSeqi NP_416277.1. NC_000913.3.
    YP_490024.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1D6M X-ray 3.00 A 1-653 [» ]
    1I7D X-ray 2.05 A 1-653 [» ]
    2O19 X-ray 2.45 A/B 1-653 [» ]
    2O54 X-ray 2.50 A/B 1-653 [» ]
    2O59 X-ray 2.50 A/B 1-653 [» ]
    2O5C X-ray 2.35 A/B 1-653 [» ]
    2O5E X-ray 2.50 A/B 1-653 [» ]
    ProteinModelPortali P14294.
    SMRi P14294. Positions 1-620.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-11012N.
    IntActi P14294. 39 interactions.
    MINTi MINT-1224249.
    STRINGi 511145.b1763.

    Proteomic databases

    PaxDbi P14294.
    PRIDEi P14294.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74833 ; AAC74833 ; b1763 .
    BAA15551 ; BAA15551 ; BAA15551 .
    GeneIDi 12930143.
    946141.
    KEGGi ecj:Y75_p1738.
    eco:b1763.
    PATRICi 32118837. VBIEscCol129921_1836.

    Organism-specific databases

    EchoBASEi EB1007.
    EcoGenei EG11014. topB.

    Phylogenomic databases

    eggNOGi COG0550.
    HOGENOMi HOG000086848.
    KOi K03169.
    OMAi SNRDFIP.
    OrthoDBi EOG60CWM6.
    PhylomeDBi P14294.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11014-MONOMER.
    ECOL316407:JW1752-MONOMER.
    MetaCyc:EG11014-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P14294.
    PROi P14294.

    Gene expression databases

    Genevestigatori P14294.

    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. "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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. 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.

    Entry informationi

    Entry nameiTOP3_ECOLI
    AccessioniPrimary (citable) accession number: P14294
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 1, 1990
    Last modified: October 1, 2014
    This is version 137 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3