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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

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

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)DescriptionActionsGraphical viewLength
    Metal bindingi22Zinc1 Publication1
    Metal bindingi57Zinc1 Publication1
    Metal bindingi177Zinc1 Publication1
    Metal bindingi234Zinc1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionDioxygenase, Oxidoreductase
    LigandMetal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11166-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001694051 – 2714,5-DOPA dioxygenase extradiolAdd BLAST271

    Proteomic databases

    PaxDbiP24197.
    PRIDEiP24197.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi4263035. 3 interactors.
    IntActiP24197. 3 interactors.
    STRINGi511145.b3039.

    Structurei

    Secondary structure

    1271
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi17 – 21Combined sources5
    Helixi33 – 44Combined sources12
    Beta strandi49 – 66Combined sources18
    Helixi95 – 105Combined sources11
    Beta strandi110 – 115Combined sources6
    Helixi121 – 130Combined sources10
    Beta strandi138 – 144Combined sources7
    Helixi149 – 159Combined sources11
    Helixi160 – 165Combined sources6
    Beta strandi167 – 173Combined sources7
    Beta strandi184 – 186Combined sources3
    Helixi192 – 202Combined sources11
    Turni203 – 206Combined sources4
    Helixi211 – 213Combined sources3
    Turni215 – 217Combined sources3
    Helixi219 – 221Combined sources3
    Helixi225 – 228Combined sources4
    Beta strandi230 – 232Combined sources3
    Turni233 – 235Combined sources3
    Helixi236 – 243Combined sources8
    Beta strandi247 – 249Combined sources3
    Turni260 – 262Combined sources3
    Beta strandi268 – 270Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2PW6X-ray2.27A1-271[»]
    ProteinModelPortaliP24197.
    SMRiP24197.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP24197.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

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

    Family and domain databases

    CDDicd07363. 45_DOPA_Dioxygenase. 1 hit.
    InterProiView protein in InterPro
    IPR014436. Extradiol_dOase_DODA.
    IPR004183. Xdiol_dOase_suB.
    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
    MTPLVKDIIM SSTRMPALFL GHGSPMNVLE DNLYTRSWQK LGMTLPRPQA
    60 70 80 90 100
    IVVVSAHWFT RGTGVTAMET PPTIHDFGGF PQALYDTHYP APGSPALAQR
    110 120 130 140 150
    LVELLAPIPV TLDKEAWGFD HGSWGVLIKM YPDADIPMVQ LSIDSSKPAA
    160 170 180 190 200
    WHFEMGRKLA ALRDEGIMLV ASGNVVHNLR TVKWHGDSSP YPWATSFNEY
    210 220 230 240 250
    VKANLTWQGP VEQHPLVNYL DHEGGTLSNP TPEHYLPLLY VLGAWDGQEP
    260 270
    ITIPVEGIEM GSLSMLSVQI G
    Length:271
    Mass (Da):29,903
    Last modified:November 2, 2016 - v4
    Checksum:iA74E9035BAF6EB0F
    GO

    Sequence cautioni

    The sequence AAC76075 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti243 – 270GAWDG…LSVQI → RYVGWAGANYHS in AAA71877 (PubMed:1314093).CuratedAdd BLAST28

    Sequence databases

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

    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.
    U28377 Genomic DNA. Translation: AAA69207.1.
    U00096 Genomic DNA. Translation: AAC76075.2. Different initiation.
    AP009048 Genomic DNA. Translation: BAE77095.1.
    PIRiE65091.
    RefSeqiNP_417511.2. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2PW6X-ray2.27A1-271[»]
    ProteinModelPortaliP24197.
    SMRiP24197.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263035. 3 interactors.
    IntActiP24197. 3 interactors.
    STRINGi511145.b3039.

    Proteomic databases

    PaxDbiP24197.
    PRIDEiP24197.

    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.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11166-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP24197.
    PROiPR:P24197.

    Family and domain databases

    CDDicd07363. 45_DOPA_Dioxygenase. 1 hit.
    InterProiView protein in InterPro
    IPR014436. Extradiol_dOase_DODA.
    IPR004183. Xdiol_dOase_suB.
    PIRSFiPIRSF006157. Doxgns_DODA. 1 hit.
    SUPFAMiSSF53213. SSF53213. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYGID_ECOLI
    AccessioniPrimary (citable) accession number: P24197
    Secondary accession number(s): Q2M9G1
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 1992
    Last sequence update: November 2, 2016
    Last modified: May 10, 2017
    This is version 124 of the entry and version 4 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    It is uncertain whether Met-1 or Met-10 is the initiator.Curated

    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.