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P20083

- PARE_ECOLI

UniProt

P20083 - PARE_ECOLI

Protein

DNA topoisomerase 4 subunit B

Gene

parE

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 133 (01 Oct 2014)
      Sequence version 3 (01 Feb 1994)
      Previous versions | rss
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    Functioni

    Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule. MukB stimulates the relaxation activity of topoisomerase IV and also has a modest effect on decatenation.3 PublicationsUniRule annotation

    Catalytic activityi

    ATP-dependent breakage, passage and rejoining of double-stranded DNA.2 PublicationsUniRule annotation

    Cofactori

    Magnesium. Binds two Mg2+ 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
    Binding sitei5 – 51ATP
    Binding sitei42 – 421ATP
    Binding sitei69 – 691ATP
    Binding sitei334 – 3341ATP
    Metal bindingi418 – 4181Magnesium 1; catalyticUniRule annotation
    Sitei443 – 4431Interaction with DNAUniRule annotation
    Sitei446 – 4461Interaction with DNAUniRule annotation
    Metal bindingi490 – 4901Magnesium 1; catalyticUniRule annotation
    Metal bindingi490 – 4901Magnesium 2UniRule annotation
    Metal bindingi492 – 4921Magnesium 2UniRule annotation
    Sitei497 – 4971Interaction with DNAUniRule annotation
    Sitei615 – 6151Interaction with DNAUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi110 – 1167ATP

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. DNA binding Source: UniProtKB-HAMAP
    3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: RefGenome
    4. magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. ATP catabolic process Source: GOC
    2. chromosome organization Source: EcoliWiki
    3. DNA topological change Source: RefGenome
    4. DNA unwinding involved in DNA replication Source: RefGenome
    5. plasmid partitioning Source: EcoliWiki
    6. response to antibiotic Source: UniProtKB-KW
    7. sister chromatid cohesion Source: EcoliWiki

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Biological processi

    Antibiotic resistance

    Keywords - Ligandi

    ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10687-MONOMER.
    ECOL316407:JW2998-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 4 subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
    Alternative name(s):
    Topoisomerase IV subunit BUniRule annotation
    Gene namesi
    Name:parEUniRule annotation
    Synonyms:nfxD
    Ordered Locus Names:b3030, JW2998
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10687. parE.

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro
    2. DNA topoisomerase complex (ATP-hydrolyzing) Source: RefGenome
    3. nucleoid Source: RefGenome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 630630DNA topoisomerase 4 subunit BPRO_0000145427Add
    BLAST

    Proteomic databases

    PaxDbiP20083.
    PRIDEiP20083.

    Expressioni

    Gene expression databases

    GenevestigatoriP20083.

    Interactioni

    Subunit structurei

    Heterotetramer composed of ParC and ParE.2 PublicationsUniRule annotation

    Protein-protein interaction databases

    DIPiDIP-10441N.
    IntActiP20083. 24 interactions.
    MINTiMINT-1223307.
    STRINGi511145.b3030.

    Structurei

    Secondary structure

    1
    630
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi7 – 93
    Helixi17 – 215
    Helixi23 – 253
    Helixi33 – 4816
    Beta strandi53 – 597
    Beta strandi65 – 695
    Turni80 – 823
    Beta strandi83 – 853
    Helixi86 – 927
    Beta strandi96 – 983
    Beta strandi100 – 1045
    Beta strandi106 – 1083
    Helixi117 – 1215
    Beta strandi123 – 13210
    Beta strandi135 – 1428
    Beta strandi145 – 15511
    Beta strandi162 – 1698
    Helixi171 – 1733
    Helixi181 – 19414
    Beta strandi199 – 2046
    Turni205 – 2084
    Beta strandi209 – 2135
    Helixi219 – 2279
    Beta strandi233 – 24311
    Beta strandi245 – 25511
    Beta strandi264 – 2685
    Helixi278 – 29720
    Helixi309 – 3135
    Beta strandi316 – 32611
    Beta strandi329 – 3313
    Helixi342 – 35918
    Helixi362 – 38221

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1S14X-ray2.00A/B1-217[»]
    1S16X-ray2.10A/B1-390[»]
    3FV5X-ray1.80A/B15-215[»]
    4HZ0X-ray2.20A/B12-216[»]
    ProteinModelPortaliP20083.
    SMRiP20083. Positions 4-383, 388-623.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP20083.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini412 – 525114ToprimUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the type II topoisomerase family. ParE type 1 subfamily.UniRule annotation
    Contains 1 Toprim domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0187.
    HOGENOMiHOG000075154.
    KOiK02622.
    OMAiQSYNADA.
    OrthoDBiEOG6P334W.
    PhylomeDBiP20083.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.30.565.10. 1 hit.
    3.40.50.670. 1 hit.
    HAMAPiMF_00938. ParE_type1.
    InterProiIPR002288. DNA_gyrase_B_C.
    IPR003594. HATPase_ATP-bd.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
    IPR001241. Topo_IIA.
    IPR013506. Topo_IIA_bsu_dom2.
    IPR013759. Topo_IIA_cen_dom.
    IPR013760. Topo_IIA_like_dom.
    IPR018522. TopoIIA_CS.
    IPR005737. TopoIV_B_Gneg.
    IPR006171. Toprim_domain.
    [Graphical view]
    PfamiPF00204. DNA_gyraseB. 1 hit.
    PF00986. DNA_gyraseB_C. 1 hit.
    PF02518. HATPase_c. 1 hit.
    PF01751. Toprim. 1 hit.
    [Graphical view]
    PRINTSiPR00418. TPI2FAMILY.
    SMARTiSM00387. HATPase_c. 1 hit.
    SM00433. TOP2c. 1 hit.
    [Graphical view]
    SUPFAMiSSF54211. SSF54211. 1 hit.
    SSF55874. SSF55874. 1 hit.
    SSF56719. SSF56719. 1 hit.
    TIGRFAMsiTIGR01055. parE_Gneg. 1 hit.
    PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P20083-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTQTYNADAI EVLTGLEPVR RRPGMYTDTT RPNHLGQEVI DNSVDEALAG    50
    HAKRVDVILH ADQSLEVIDD GRGMPVDIHP EEGVPAVELI LCRLHAGGKF 100
    SNKNYQFSGG LHGVGISVVN ALSKRVEVNV RRDGQVYNIA FENGEKVQDL 150
    QVVGTCGKRN TGTSVHFWPD ETFFDSPRFS VSRLTHVLKA KAVLCPGVEI 200
    TFKDEINNTE QRWCYQDGLN DYLAEAVNGL PTLPEKPFIG NFAGDTEAVD 250
    WALLWLPEGG ELLTESYVNL IPTMQGGTHV NGLRQGLLDA MREFCEYRNI 300
    LPRGVKLSAE DIWDRCAYVL SVKMQDPQFA GQTKERLSSR QCAAFVSGVV 350
    KDAFILWLNQ NVQAAELLAE MAISSAQRRM RAAKKVVRKK LTSGPALPGK 400
    LADCTAQDLN RTELFLVEGD SAGGSAKQAR DREYQAIMPL KGKILNTWEV 450
    SSDEVLASQE VHDISVAIGI DPDSDDLSQL RYGKICILAD ADSDGLHIAT 500
    LLCALFVKHF RALVKHGHVY VALPPLYRID LGKEVYYALT EEEKEGVLEQ 550
    LKRKKGKPNV QRFKGLGEMN PMQLRETTLD PNTRRLVQLT IDDEDDQRTD 600
    AMMDMLLAKK RSEDRRNWLQ EKGDMAEIEV 630
    Length:630
    Mass (Da):70,244
    Last modified:February 1, 1994 - v3
    Checksum:i3F83D108BC1C6A41
    GO

    Sequence cautioni

    The sequence AAA24298.1 differs from that shown. Reason: Frameshift at position 597.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti445 – 4451L → H in strain: DH161; quinolone-resistant. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M58409 Genomic DNA. Translation: AAA24298.1. Frameshift.
    U28377 Genomic DNA. Translation: AAA69198.1.
    U00096 Genomic DNA. Translation: AAC76066.1.
    AP009048 Genomic DNA. Translation: BAE77086.1.
    L22026 Unassigned DNA. Translation: AAC36841.1.
    PIRiD65090.
    RefSeqiNP_417502.1. NC_000913.3.
    YP_491222.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76066; AAC76066; b3030.
    BAE77086; BAE77086; BAE77086.
    GeneIDi12933399.
    947501.
    KEGGiecj:Y75_p2956.
    eco:b3030.
    PATRICi32121470. VBIEscCol129921_3122.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M58409 Genomic DNA. Translation: AAA24298.1 . Frameshift.
    U28377 Genomic DNA. Translation: AAA69198.1 .
    U00096 Genomic DNA. Translation: AAC76066.1 .
    AP009048 Genomic DNA. Translation: BAE77086.1 .
    L22026 Unassigned DNA. Translation: AAC36841.1 .
    PIRi D65090.
    RefSeqi NP_417502.1. NC_000913.3.
    YP_491222.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1S14 X-ray 2.00 A/B 1-217 [» ]
    1S16 X-ray 2.10 A/B 1-390 [» ]
    3FV5 X-ray 1.80 A/B 15-215 [» ]
    4HZ0 X-ray 2.20 A/B 12-216 [» ]
    ProteinModelPortali P20083.
    SMRi P20083. Positions 4-383, 388-623.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10441N.
    IntActi P20083. 24 interactions.
    MINTi MINT-1223307.
    STRINGi 511145.b3030.

    Chemistry

    BindingDBi P20083.
    ChEMBLi CHEMBL2363076.

    Proteomic databases

    PaxDbi P20083.
    PRIDEi P20083.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76066 ; AAC76066 ; b3030 .
    BAE77086 ; BAE77086 ; BAE77086 .
    GeneIDi 12933399.
    947501.
    KEGGi ecj:Y75_p2956.
    eco:b3030.
    PATRICi 32121470. VBIEscCol129921_3122.

    Organism-specific databases

    EchoBASEi EB0681.
    EcoGenei EG10687. parE.

    Phylogenomic databases

    eggNOGi COG0187.
    HOGENOMi HOG000075154.
    KOi K02622.
    OMAi QSYNADA.
    OrthoDBi EOG6P334W.
    PhylomeDBi P20083.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10687-MONOMER.
    ECOL316407:JW2998-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P20083.
    PROi P20083.

    Gene expression databases

    Genevestigatori P20083.

    Family and domain databases

    Gene3Di 3.30.230.10. 1 hit.
    3.30.565.10. 1 hit.
    3.40.50.670. 1 hit.
    HAMAPi MF_00938. ParE_type1.
    InterProi IPR002288. DNA_gyrase_B_C.
    IPR003594. HATPase_ATP-bd.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
    IPR001241. Topo_IIA.
    IPR013506. Topo_IIA_bsu_dom2.
    IPR013759. Topo_IIA_cen_dom.
    IPR013760. Topo_IIA_like_dom.
    IPR018522. TopoIIA_CS.
    IPR005737. TopoIV_B_Gneg.
    IPR006171. Toprim_domain.
    [Graphical view ]
    Pfami PF00204. DNA_gyraseB. 1 hit.
    PF00986. DNA_gyraseB_C. 1 hit.
    PF02518. HATPase_c. 1 hit.
    PF01751. Toprim. 1 hit.
    [Graphical view ]
    PRINTSi PR00418. TPI2FAMILY.
    SMARTi SM00387. HATPase_c. 1 hit.
    SM00433. TOP2c. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54211. SSF54211. 1 hit.
    SSF55874. SSF55874. 1 hit.
    SSF56719. SSF56719. 1 hit.
    TIGRFAMsi TIGR01055. parE_Gneg. 1 hit.
    PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "New topoisomerase essential for chromosome segregation in E. coli."
      Kato J., Nishimura Y., Imamura R., Niki H., Hiraga S., Suzuki H.
      Cell 63:393-404(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-602.
      Strain: K12.
    2. "Molecular characterization of the Salmonella typhimurium parE gene."
      Springer A.L., Schmid M.B.
      Nucleic Acids Res. 21:1805-1809(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: SEQUENCE REVISION TO C-TERMINUS.
    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 topoisomerase IV. Purification, characterization, subunit structure, and subunit interactions."
      Peng H., Marians K.J.
      J. Biol. Chem. 268:24481-24490(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 588-630, CHARACTERIZATION.
      Strain: K12.
    6. "Use of divalent metal ions in the DNA cleavage reaction of topoisomerase IV."
      Pitts S.L., Liou G.F., Mitchenall L.A., Burgin A.B., Maxwell A., Neuman K.C., Osheroff N.
      Nucleic Acids Res. 39:4808-4817(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT, COFACTOR, PUTATIVE METAL-BINDING SITES, CATALYTIC ACTIVITY.
    7. "Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase."
      Bellon S., Parsons J.D., Wei Y., Hayakawa K., Swenson L.L., Charifson P.S., Lippke J.A., Aldape R., Gross C.H.
      Antimicrob. Agents Chemother. 48:1856-1864(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-390 IN COMPLEXES WITH NOVOBIOCIN AND ADENYLYL-IMIDODIPHOSPHATE, CATALYTIC ACTIVITY, FUNCTION, SUBUNIT.
    8. "Quinolone resistance locus nfxD of Escherichia coli is a mutant allele of the parE gene encoding a subunit of topoisomerase IV."
      Breines D.M., Ouabdesselam S., Ng E.Y., Tankovic J., Shah S., Soussy C.J., Hooper D.C.
      Antimicrob. Agents Chemother. 41:175-179(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT QUINOLONE-RESISTANT HIS-445.
    9. "Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction."
      Li Y., Stewart N.K., Berger A.J., Vos S., Schoeffler A.J., Berger J.M., Chait B.T., Oakley M.G.
      Proc. Natl. Acad. Sci. U.S.A. 107:18832-18837(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION MODIFIED BY MUKB.

    Entry informationi

    Entry nameiPARE_ECOLI
    AccessioniPrimary (citable) accession number: P20083
    Secondary accession number(s): Q2M9H0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1991
    Last sequence update: February 1, 1994
    Last modified: October 1, 2014
    This is version 133 of the entry and version 3 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. 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