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Protein

3-keto-L-gulonate-6-phosphate decarboxylase UlaD

Gene

ulaD

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

Functioni

Catalyzes the decarboxylation of 3-keto-L-gulonate-6-P into L-xylulose-5-P. Is involved in the anaerobic L-ascorbate utilization.1 Publication

Catalytic activityi

3-dehydro-L-gulonate 6-phosphate = L-xylulose 5-phosphate + CO2.

Cofactori

Mg2+Note: Binds 1 Mg2+ ion per subunit.

Kineticsi

  1. KM=0.67 mM for 3-keto-L-gulonate-6-P1 Publication

    Pathwayi: L-ascorbate degradation

    This protein is involved in step 2 of the subpathway that synthesizes D-xylulose 5-phosphate from L-ascorbate.
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. Probable L-ascorbate-6-phosphate lactonase UlaG (ulaG)
    2. 3-keto-L-gulonate-6-phosphate decarboxylase UlaD (ulaD)
    3. L-ribulose-5-phosphate 3-epimerase UlaE (ulaE)
    4. L-ribulose-5-phosphate 4-epimerase UlaF (ulaF)
    This subpathway is part of the pathway L-ascorbate degradation, which is itself part of Cofactor degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-xylulose 5-phosphate from L-ascorbate, the pathway L-ascorbate degradation and in Cofactor degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei11Substrate1
    Metal bindingi33Magnesium1
    Metal bindingi62Magnesium1
    Sitei64Transition state stabilizer1
    Sitei67Transition state stabilizer1
    Binding sitei192Substrate1

    GO - Molecular functioni

    • 3-dehydro-L-gulonate-6-phosphate decarboxylase activity Source: EcoCyc
    • magnesium ion binding Source: EcoCyc
    • orotidine-5'-phosphate decarboxylase activity Source: InterPro

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Carbohydrate metabolism

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7858-MONOMER.
    ECOL316407:JW4154-MONOMER.
    MetaCyc:G7858-MONOMER.
    BRENDAi4.1.1.85. 2026.
    SABIO-RKP39304.
    UniPathwayiUPA00263; UER00378.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-keto-L-gulonate-6-phosphate decarboxylase UlaD (EC:4.1.1.85)
    Alternative name(s):
    3-dehydro-L-gulonate-6-phosphate decarboxylase
    KGPDC
    L-ascorbate utilization protein D
    Gene namesi
    Name:ulaD
    Synonyms:sgaH, yjfV
    Ordered Locus Names:b4196, JW4154
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12496. ulaD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi33E → K: Loss of activity. 1 Publication1
    Mutagenesisi64K → A: 16% of wild-type activity. 1 Publication1
    Mutagenesisi67D → A: 5% of wild-type activity. 1 Publication1
    Mutagenesisi112E → A: 0.5% of wild-type activity. 1 Publication1
    Mutagenesisi136H → A: 5% of wild-type activity. 1 Publication1
    Mutagenesisi139R → V: 17% of wild-type activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002121031 – 2163-keto-L-gulonate-6-phosphate decarboxylase UlaDAdd BLAST216

    Proteomic databases

    PaxDbiP39304.
    PRIDEiP39304.

    2D gel databases

    SWISS-2DPAGEP39304.

    Expressioni

    Inductioni

    Induced by L-ascorbate. Repressed by UlaR.2 Publications

    Interactioni

    Subunit structurei

    Homodimer.3 Publications

    Protein-protein interaction databases

    BioGridi4262000. 10 interactors.
    DIPiDIP-10869N.
    IntActiP39304. 1 interactor.
    STRINGi511145.b4196.

    Structurei

    Secondary structure

    1216
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 10Combined sources6
    Helixi15 – 25Combined sources11
    Helixi26 – 28Combined sources3
    Beta strandi30 – 34Combined sources5
    Helixi36 – 42Combined sources7
    Helixi45 – 53Combined sources9
    Beta strandi57 – 65Combined sources9
    Helixi69 – 78Combined sources10
    Beta strandi82 – 87Combined sources6
    Helixi92 – 104Combined sources13
    Beta strandi108 – 113Combined sources6
    Helixi119 – 127Combined sources9
    Beta strandi132 – 136Combined sources5
    Helixi139 – 143Combined sources5
    Helixi150 – 161Combined sources12
    Beta strandi165 – 171Combined sources7
    Helixi174 – 180Combined sources7
    Beta strandi186 – 191Combined sources6
    Helixi192 – 195Combined sources4
    Beta strandi197 – 199Combined sources3
    Helixi200 – 214Combined sources15

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1KV8X-ray1.62A/B1-216[»]
    1KW1X-ray2.20A/B1-216[»]
    1Q6LX-ray1.80A/B1-216[»]
    1Q6OX-ray1.20A/B1-216[»]
    1Q6QX-ray1.70A/B1-216[»]
    1Q6RX-ray1.76A/B1-216[»]
    1SO3X-ray1.90A/B1-216[»]
    1SO4X-ray1.70A/B1-216[»]
    1SO5X-ray1.80A/B1-216[»]
    1SO6X-ray1.90A/B1-216[»]
    1XBVX-ray1.66A/B1-216[»]
    1XBXX-ray1.81A/B1-216[»]
    1XBYX-ray1.58A/B1-216[»]
    1XBZX-ray1.80A/B1-216[»]
    ProteinModelPortaliP39304.
    SMRiP39304.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39304.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the HPS/KGPDC family. KGPDC subfamily.Curated

    Phylogenomic databases

    eggNOGiENOG4105H6Q. Bacteria.
    COG0269. LUCA.
    HOGENOMiHOG000226068.
    InParanoidiP39304.
    KOiK03078.
    OMAiTIPTMKA.
    PhylomeDBiP39304.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01267. UlaD. 1 hit.
    InterProiIPR023942. 3-keto-L-gulonate6Pdecase_UlaD.
    IPR013785. Aldolase_TIM.
    IPR001754. OMPdeCOase_dom.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view]
    PfamiPF00215. OMPdecase. 1 hit.
    [Graphical view]
    SMARTiSM00934. OMPdecase. 1 hit.
    [Graphical view]
    SUPFAMiSSF51366. SSF51366. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P39304-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSLPMLQVAL DNQTMDSAYE TTRLIAEEVD IIEVGTILCV GEGVRAVRDL
    60 70 80 90 100
    KALYPHKIVL ADAKIADAGK ILSRMCFEAN ADWVTVICCA DINTAKGALD
    110 120 130 140 150
    VAKEFNGDVQ IELTGYWTWE QAQQWRDAGI GQVVYHRSRD AQAAGVAWGE
    160 170 180 190 200
    ADITAIKRLS DMGFKVTVTG GLALEDLPLF KGIPIHVFIA GRSIRDAASP
    210
    VEAARQFKRS IAELWG
    Length:216
    Mass (Da):23,578
    Last modified:February 1, 1995 - v1
    Checksum:iEC8490DA1D02D824
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U14003 Genomic DNA. Translation: AAA97092.1.
    U00096 Genomic DNA. Translation: AAC77153.1.
    AP009048 Genomic DNA. Translation: BAE78197.1.
    PIRiS56421.
    RefSeqiNP_418617.1. NC_000913.3.
    WP_000056749.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77153; AAC77153; b4196.
    BAE78197; BAE78197; BAE78197.
    GeneIDi948714.
    KEGGiecj:JW4154.
    eco:b4196.
    PATRICi32123967. VBIEscCol129921_4328.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U14003 Genomic DNA. Translation: AAA97092.1.
    U00096 Genomic DNA. Translation: AAC77153.1.
    AP009048 Genomic DNA. Translation: BAE78197.1.
    PIRiS56421.
    RefSeqiNP_418617.1. NC_000913.3.
    WP_000056749.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1KV8X-ray1.62A/B1-216[»]
    1KW1X-ray2.20A/B1-216[»]
    1Q6LX-ray1.80A/B1-216[»]
    1Q6OX-ray1.20A/B1-216[»]
    1Q6QX-ray1.70A/B1-216[»]
    1Q6RX-ray1.76A/B1-216[»]
    1SO3X-ray1.90A/B1-216[»]
    1SO4X-ray1.70A/B1-216[»]
    1SO5X-ray1.80A/B1-216[»]
    1SO6X-ray1.90A/B1-216[»]
    1XBVX-ray1.66A/B1-216[»]
    1XBXX-ray1.81A/B1-216[»]
    1XBYX-ray1.58A/B1-216[»]
    1XBZX-ray1.80A/B1-216[»]
    ProteinModelPortaliP39304.
    SMRiP39304.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262000. 10 interactors.
    DIPiDIP-10869N.
    IntActiP39304. 1 interactor.
    STRINGi511145.b4196.

    2D gel databases

    SWISS-2DPAGEP39304.

    Proteomic databases

    PaxDbiP39304.
    PRIDEiP39304.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77153; AAC77153; b4196.
    BAE78197; BAE78197; BAE78197.
    GeneIDi948714.
    KEGGiecj:JW4154.
    eco:b4196.
    PATRICi32123967. VBIEscCol129921_4328.

    Organism-specific databases

    EchoBASEiEB2389.
    EcoGeneiEG12496. ulaD.

    Phylogenomic databases

    eggNOGiENOG4105H6Q. Bacteria.
    COG0269. LUCA.
    HOGENOMiHOG000226068.
    InParanoidiP39304.
    KOiK03078.
    OMAiTIPTMKA.
    PhylomeDBiP39304.

    Enzyme and pathway databases

    UniPathwayiUPA00263; UER00378.
    BioCyciEcoCyc:G7858-MONOMER.
    ECOL316407:JW4154-MONOMER.
    MetaCyc:G7858-MONOMER.
    BRENDAi4.1.1.85. 2026.
    SABIO-RKP39304.

    Miscellaneous databases

    EvolutionaryTraceiP39304.
    PROiP39304.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01267. UlaD. 1 hit.
    InterProiIPR023942. 3-keto-L-gulonate6Pdecase_UlaD.
    IPR013785. Aldolase_TIM.
    IPR001754. OMPdeCOase_dom.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view]
    PfamiPF00215. OMPdecase. 1 hit.
    [Graphical view]
    SMARTiSM00934. OMPdecase. 1 hit.
    [Graphical view]
    SUPFAMiSSF51366. SSF51366. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiULAD_ECOLI
    AccessioniPrimary (citable) accession number: P39304
    Secondary accession number(s): Q2M6A9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: November 2, 2016
    This is version 134 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The reaction mechanism proceeds via the formation of a Mg2+ ion-stabilized 1,2-cis-enediolate intermediate. Water molecules competitively shuttle protons from the side chains of His-136 and Arg-139 to alternate faces of this intermediate. The active site is located at the interface of the component polypeptides.

    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

    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.