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P0AAB4

- UBID_ECOLI

UniProt

P0AAB4 - UBID_ECOLI

Protein

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

Gene

ubiD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 84 (01 Oct 2014)
      Sequence version 1 (13 Sep 2005)
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    Functioni

    Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol.1 Publication

    Cofactori

    Divalent metal ions. Preferably manganese.1 Publication

    Enzyme regulationi

    Requires phospholipid, a metal ion, dithiothreitol and at least one other so far unidentified soluble cofactor for maximal activity. Inhibited by EDTA.1 Publication

    Pathwayi

    GO - Molecular functioni

    1. 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity Source: EcoCyc
    2. FMN binding Source: InterPro
    3. identical protein binding Source: EcoCyc
    4. oxidoreductase activity Source: InterPro

    GO - Biological processi

    1. ubiquinone biosynthetic process Source: EcoCyc

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Ubiquinone biosynthesis

    Keywords - Ligandi

    Manganese

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11396-MONOMER.
    ECOL316407:JW3819-MONOMER.
    MetaCyc:EG11396-MONOMER.
    UniPathwayiUPA00232.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC:4.1.1.-)
    Alternative name(s):
    Polyprenyl p-hydroxybenzoate decarboxylase
    Gene namesi
    Name:ubiD
    Synonyms:yigC, yigY
    Ordered Locus Names:b3843, JW3819
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11396. ubiD.

    Subcellular locationi

    Cell membrane 1 Publication; Peripheral membrane protein 1 Publication

    GO - Cellular componenti

    1. plasma membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell membrane, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 4974973-octaprenyl-4-hydroxybenzoate carboxy-lyasePRO_0000157357Add
    BLAST

    Proteomic databases

    PaxDbiP0AAB4.
    PRIDEiP0AAB4.

    Expressioni

    Gene expression databases

    GenevestigatoriP0AAB4.

    Interactioni

    Subunit structurei

    Homohexamer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-48249N.
    IntActiP0AAB4. 4 interactions.
    STRINGi511145.b3843.

    Structurei

    Secondary structure

    1
    497
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 1810
    Beta strandi22 – 254
    Helixi34 – 4310
    Beta strandi49 – 535
    Beta strandi62 – 643
    Helixi70 – 756
    Turni76 – 783
    Helixi82 – 843
    Helixi85 – 9612
    Beta strandi123 – 1275
    Helixi129 – 1313
    Beta strandi132 – 1365
    Helixi137 – 1393
    Helixi142 – 1443
    Beta strandi163 – 1675
    Beta strandi174 – 1774
    Beta strandi181 – 1833
    Beta strandi185 – 1917
    Beta strandi195 – 1973
    Helixi198 – 20912
    Beta strandi215 – 2228
    Helixi225 – 2328
    Helixi241 – 2499
    Beta strandi254 – 2574
    Beta strandi259 – 2624
    Beta strandi264 – 2663
    Beta strandi270 – 28516
    Beta strandi293 – 2964
    Beta strandi299 – 31113
    Beta strandi324 – 3263
    Helixi328 – 34720
    Beta strandi351 – 3555
    Helixi358 – 3603
    Turni361 – 3633
    Beta strandi364 – 3707
    Helixi377 – 38711
    Helixi390 – 3923
    Beta strandi397 – 4026
    Helixi410 – 41910
    Helixi423 – 4264
    Beta strandi427 – 4348
    Beta strandi442 – 4443
    Beta strandi447 – 4548
    Beta strandi463 – 4653
    Helixi475 – 48410
    Turni485 – 4873

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2IDBX-ray2.90A/B/C1-497[»]
    ProteinModelPortaliP0AAB4.
    SMRiP0AAB4. Positions 6-491.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AAB4.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the UbiD family.Curated

    Phylogenomic databases

    eggNOGiCOG0043.
    KOiK03182.
    OMAiSKMGMDA.
    OrthoDBiEOG6QZMM7.
    PhylomeDBiP0AAB4.

    Family and domain databases

    HAMAPiMF_01636. UbiD.
    InterProiIPR023677. OPHB_Carboxy-lyase.
    IPR012349. Split_barrel_FMN-bd.
    IPR002830. UbiD.
    [Graphical view]
    PfamiPF01977. UbiD. 1 hit.
    [Graphical view]
    SUPFAMiSSF50475. SSF50475. 1 hit.
    TIGRFAMsiTIGR00148. TIGR00148. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0AAB4-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDAMKYNDLR DFLTLLEQQG ELKRITLPVD PHLEITEIAD RTLRAGGPAL    50
    LFENPKGYSM PVLCNLFGTP KRVAMGMGQE DVSALREVGK LLAFLKEPEP 100
    PKGFRDLFDK LPQFKQVLNM PTKRLRGAPC QQKIVSGDDV DLNRIPIMTC 150
    WPEDAAPLIT WGLTVTRGPH KERQNLGIYR QQLIGKNKLI MRWLSHRGGA 200
    LDYQEWCAAH PGERFPVSVA LGADPATILG AVTPVPDTLS EYAFAGLLRG 250
    TKTEVVKCIS NDLEVPASAE IVLEGYIEQG ETAPEGPYGD HTGYYNEVDS 300
    FPVFTVTHIT QREDAIYHST YTGRPPDEPA VLGVALNEVF VPILQKQFPE 350
    IVDFYLPPEG CSYRLAVVTI KKQYAGHAKR VMMGVWSFLR QFMYTKFVIV 400
    CDDDVNARDW NDVIWAITTR MDPARDTVLV ENTPIDYLDF ASPVSGLGSK 450
    MGLDATNKWP GETQREWGRP IKKDPDVVAH IDAIWDELAI FNNGKSA 497
    Length:497
    Mass (Da):55,604
    Last modified:September 13, 2005 - v1
    Checksum:i5432A3BEBE81ECC5
    GO

    Sequence cautioni

    The sequence AAA67639.1 differs from that shown. Reason: Frameshift at position 380.
    The sequence CAA46146.1 differs from that shown. Reason: Frameshift at position 376.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti452 – 4521G → R in AN66; inactive protein. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X65013 Genomic DNA. Translation: CAA46146.1. Frameshift.
    M87049 Genomic DNA. Translation: AAA67639.1. Frameshift.
    M87049 Genomic DNA. Translation: AAA67640.1.
    U00096 Genomic DNA. Translation: AAC76846.1.
    AP009048 Genomic DNA. Translation: BAE77460.1.
    PIRiD65189.
    S20905.
    S30734.
    RefSeqiNP_418285.1. NC_000913.3.
    YP_491601.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76846; AAC76846; b3843.
    BAE77460; BAE77460; BAE77460.
    GeneIDi12932472.
    948326.
    KEGGiecj:Y75_p3337.
    eco:b3843.
    PATRICi32123183. VBIEscCol129921_3957.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X65013 Genomic DNA. Translation: CAA46146.1 . Frameshift.
    M87049 Genomic DNA. Translation: AAA67639.1 . Frameshift.
    M87049 Genomic DNA. Translation: AAA67640.1 .
    U00096 Genomic DNA. Translation: AAC76846.1 .
    AP009048 Genomic DNA. Translation: BAE77460.1 .
    PIRi D65189.
    S20905.
    S30734.
    RefSeqi NP_418285.1. NC_000913.3.
    YP_491601.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2IDB X-ray 2.90 A/B/C 1-497 [» ]
    ProteinModelPortali P0AAB4.
    SMRi P0AAB4. Positions 6-491.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48249N.
    IntActi P0AAB4. 4 interactions.
    STRINGi 511145.b3843.

    Proteomic databases

    PaxDbi P0AAB4.
    PRIDEi P0AAB4.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76846 ; AAC76846 ; b3843 .
    BAE77460 ; BAE77460 ; BAE77460 .
    GeneIDi 12932472.
    948326.
    KEGGi ecj:Y75_p3337.
    eco:b3843.
    PATRICi 32123183. VBIEscCol129921_3957.

    Organism-specific databases

    EchoBASEi EB1369.
    EcoGenei EG11396. ubiD.

    Phylogenomic databases

    eggNOGi COG0043.
    KOi K03182.
    OMAi SKMGMDA.
    OrthoDBi EOG6QZMM7.
    PhylomeDBi P0AAB4.

    Enzyme and pathway databases

    UniPathwayi UPA00232 .
    BioCyci EcoCyc:EG11396-MONOMER.
    ECOL316407:JW3819-MONOMER.
    MetaCyc:EG11396-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0AAB4.
    PROi P0AAB4.

    Gene expression databases

    Genevestigatori P0AAB4.

    Family and domain databases

    HAMAPi MF_01636. UbiD.
    InterProi IPR023677. OPHB_Carboxy-lyase.
    IPR012349. Split_barrel_FMN-bd.
    IPR002830. UbiD.
    [Graphical view ]
    Pfami PF01977. UbiD. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50475. SSF50475. 1 hit.
    TIGRFAMsi TIGR00148. TIGR00148. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Escherichia coli HlyT protein, a transcriptional activator of haemolysin synthesis and secretion, is encoded by the rfaH (sfrB) locus required for expression of sex factor and lipopolysaccharide genes."
      Bailey M.J.A., Koronakis V., Schmoll T., Hughes C.
      Mol. Microbiol. 6:1003-1012(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 5KC.
    2. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
      Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
      Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION.
      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. "Membrane-associated reactions in ubiquinone biosynthesis in Escherichia coli. 3-Octaprenyl-4-hydroxybenzoate carboxy-lyase."
      Leppik R.A., Young I.G., Gibson F.
      Biochim. Biophys. Acta 436:800-810(1976) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, COFACTOR, ENZYME REGULATION, PATHWAY, SUBUNIT, SUBCELLULAR LOCATION.
      Strain: K12.
    6. "Identification of the ubiD gene on the Escherichia coli chromosome."
      Zhang H., Javor G.T.
      J. Bacteriol. 182:6243-6246(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION AS UBID, VARIANT AN66 ARG-452.
      Strain: K12.

    Entry informationi

    Entry nameiUBID_ECOLI
    AccessioniPrimary (citable) accession number: P0AAB4
    Secondary accession number(s): P26615
    , P27861, P76767, Q2M8E6, Q47265, Q47714
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 13, 2005
    Last sequence update: September 13, 2005
    Last modified: October 1, 2014
    This is version 84 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, Reference proteome

    Documents

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

    External Data

    Dasty 3