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Protein

4,5-DOPA dioxygenase extradiol

Gene

ygiD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

In vitro, opens the cyclic ring of dihydroxy-phenylalanine (DOPA) between carbons 4 and 5, thus producing an unstable seco-DOPA that rearranges nonenzymatically to betalamic acid. The physiological substrate is unknown.1 Publication

Catalytic activityi

L-dopa + O2 = 4-(L-alanin-3-yl)-2-hydroxy-cis,cis-muconate 6-semialdehyde.1 Publication

Cofactori

Zn2+By similarity

Kineticsi

kcat is 0.17 min(-1) with L-DOPA.1 Publication

  1. KM=7.9 mM for L-DOPA1 Publication

    pH dependencei

    Optimum pH is 8.0.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi13 – 131Zinc1 Publication
    Metal bindingi48 – 481Zinc1 Publication
    Metal bindingi168 – 1681Zinc1 Publication
    Metal bindingi225 – 2251Zinc1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Dioxygenase, Oxidoreductase

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11166-MONOMER.
    ECOL316407:JW3007-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4,5-DOPA dioxygenase extradiolCurated (EC:1.13.11.291 Publication)
    Gene namesi
    Name:ygiD
    Ordered Locus Names:b3039, JW3007
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11166. ygiD.

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    • cytoplasm Source: UniProtKB-SubCell
    • plasma membrane Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2622624,5-DOPA dioxygenase extradiolPRO_0000169405Add
    BLAST

    Proteomic databases

    EPDiP24197.
    PaxDbiP24197.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi4263035. 3 interactions.
    IntActiP24197. 3 interactions.
    STRINGi511145.b3039.

    Structurei

    Secondary structure

    1
    262
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 125Combined sources
    Helixi24 – 3512Combined sources
    Beta strandi40 – 5718Combined sources
    Helixi86 – 9611Combined sources
    Beta strandi101 – 1066Combined sources
    Helixi112 – 12110Combined sources
    Beta strandi129 – 1357Combined sources
    Helixi140 – 15011Combined sources
    Helixi151 – 1566Combined sources
    Beta strandi158 – 1647Combined sources
    Beta strandi175 – 1773Combined sources
    Helixi183 – 19311Combined sources
    Turni194 – 1974Combined sources
    Helixi202 – 2043Combined sources
    Turni206 – 2083Combined sources
    Helixi210 – 2123Combined sources
    Helixi216 – 2194Combined sources
    Beta strandi221 – 2233Combined sources
    Turni224 – 2263Combined sources
    Helixi227 – 2348Combined sources
    Beta strandi238 – 2403Combined sources
    Turni251 – 2533Combined sources
    Beta strandi259 – 2613Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PW6X-ray2.27A1-262[»]
    ProteinModelPortaliP24197.
    SMRiP24197. Positions 5-262.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP24197.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C8E. Bacteria.
    COG3384. LUCA.
    HOGENOMiHOG000236850.
    InParanoidiP24197.
    KOiK15777.
    OrthoDBiEOG6JDW8T.
    PhylomeDBiP24197.

    Family and domain databases

    Gene3Di3.40.830.10. 1 hit.
    InterProiIPR014436. Extradiol_dOase_DODA.
    IPR004183. Xdiol_dOase_suB.
    [Graphical view]
    PfamiPF02900. LigB. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006157. Doxgns_DODA. 1 hit.
    SUPFAMiSSF53213. SSF53213. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P24197-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSSTRMPALF LGHGSPMNVL EDNLYTRSWQ KLGMTLPRPQ AIVVVSAHWF
    60 70 80 90 100
    TRGTGVTAME TPPTIHDFGG FPQALYDTHY PAPGSPALAQ RLVELLAPIP
    110 120 130 140 150
    VTLDKEAWGF DHGSWGVLIK MYPDADIPMV QLSIDSSKPA AWHFEMGRKL
    160 170 180 190 200
    AALRDEGIML VASGNVVHNL RTVKWHGDSS PYPWATSFNE YVKANLTWQG
    210 220 230 240 250
    PVEQHPLVNY LDHEGGTLSN PTPEHYLPLL YVLGAWDGQE PITIPVEGIE
    260
    MGSLSMLSVQ IG
    Length:262
    Mass (Da):28,892
    Last modified:November 24, 2009 - v3
    Checksum:i7CFF9150AD49D50C
    GO

    Sequence cautioni

    The sequence AAA69207.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence AAA71877.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence BAE77095.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti234 – 26128GAWDG…LSVQI → RYVGWAGANYHS in AAA71877 (PubMed:1314093).CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M77129 Genomic DNA. Translation: AAA71877.1. Different initiation.
    U28377 Genomic DNA. Translation: AAA69207.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76075.2.
    AP009048 Genomic DNA. Translation: BAE77095.1. Different initiation.
    PIRiE65091.
    RefSeqiNP_417511.2. NC_000913.3.
    WP_001320780.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76075; AAC76075; b3039.
    BAE77095; BAE77095; BAE77095.
    GeneIDi946447.
    KEGGiecj:JW3007.
    eco:b3039.
    PATRICi32121488. VBIEscCol129921_3131.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M77129 Genomic DNA. Translation: AAA71877.1. Different initiation.
    U28377 Genomic DNA. Translation: AAA69207.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76075.2.
    AP009048 Genomic DNA. Translation: BAE77095.1. Different initiation.
    PIRiE65091.
    RefSeqiNP_417511.2. NC_000913.3.
    WP_001320780.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PW6X-ray2.27A1-262[»]
    ProteinModelPortaliP24197.
    SMRiP24197. Positions 5-262.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263035. 3 interactions.
    IntActiP24197. 3 interactions.
    STRINGi511145.b3039.

    Proteomic databases

    EPDiP24197.
    PaxDbiP24197.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76075; AAC76075; b3039.
    BAE77095; BAE77095; BAE77095.
    GeneIDi946447.
    KEGGiecj:JW3007.
    eco:b3039.
    PATRICi32121488. VBIEscCol129921_3131.

    Organism-specific databases

    EchoBASEiEB1154.
    EcoGeneiEG11166. ygiD.

    Phylogenomic databases

    eggNOGiENOG4105C8E. Bacteria.
    COG3384. LUCA.
    HOGENOMiHOG000236850.
    InParanoidiP24197.
    KOiK15777.
    OrthoDBiEOG6JDW8T.
    PhylomeDBiP24197.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11166-MONOMER.
    ECOL316407:JW3007-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP24197.
    PROiP24197.

    Family and domain databases

    Gene3Di3.40.830.10. 1 hit.
    InterProiIPR014436. Extradiol_dOase_DODA.
    IPR004183. Xdiol_dOase_suB.
    [Graphical view]
    PfamiPF02900. LigB. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006157. Doxgns_DODA. 1 hit.
    SUPFAMiSSF53213. SSF53213. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Nucleotide sequence of a region duplicated in Escherichia coli toc mutants."
      Yang T.-P., Depew R.E.
      Biochim. Biophys. Acta 1130:227-228(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "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.
    4. "Escherichia coli protein YgiD produces the structural unit of plant pigments betalains: characterization of a prokaryotic enzyme with DOPA-extradiol-dioxygenase activity."
      Gandia-Herrero F., Garcia-Carmona F.
      Appl. Microbiol. Biotechnol. 98:1165-1174(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, SUBCELLULAR LOCATION.
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Crystal structure of uncharacterized protein JW3007 from Escherichia coli K12."
      Southeast collaboratory for structural genomics (SECSG)
      Submitted (JUN-2007) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS), ZINC BINDING.

    Entry informationi

    Entry nameiYGID_ECOLI
    AccessioniPrimary (citable) accession number: P24197
    Secondary accession number(s): Q2M9G1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 1, 1992
    Last sequence update: November 24, 2009
    Last modified: March 16, 2016
    This is version 117 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Betalamic acid is the structural unit of the betalains, natural nitrogen-containing water-soluble pigments with high colorant and bioactive properties, characteristic of plants of the order Caryophyllales.1 Publication

    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.