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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

    Pathway: 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-keto-L-gulonate-6-phosphate decarboxylase UlaD (ulaD)
    3. L-ribulose-5-phosphate 3-epimerase UlaE (ulaE), L-ribulose-5-phosphate 3-epimerase UlaE (ulaE)
    4. L-ribulose-5-phosphate 4-epimerase UlaF (ulaF), 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei11 – 111Substrate
    Metal bindingi33 – 331Magnesium
    Metal bindingi62 – 621Magnesium
    Sitei64 – 641Transition state stabilizer
    Sitei67 – 671Transition state stabilizer
    Binding sitei192 – 1921Substrate

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12496. ulaD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi33 – 331E → K: Loss of activity. 1 Publication
    Mutagenesisi64 – 641K → A: 16% of wild-type activity. 1 Publication
    Mutagenesisi67 – 671D → A: 5% of wild-type activity. 1 Publication
    Mutagenesisi112 – 1121E → A: 0.5% of wild-type activity. 1 Publication
    Mutagenesisi136 – 1361H → A: 5% of wild-type activity. 1 Publication
    Mutagenesisi139 – 1391R → V: 17% of wild-type activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2162163-keto-L-gulonate-6-phosphate decarboxylase UlaDPRO_0000212103Add
    BLAST

    Proteomic databases

    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

    DIPiDIP-10869N.
    IntActiP39304. 1 interaction.
    STRINGi511145.b4196.

    Structurei

    Secondary structure

    1
    216
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106Combined sources
    Helixi15 – 2511Combined sources
    Helixi26 – 283Combined sources
    Beta strandi30 – 345Combined sources
    Helixi36 – 427Combined sources
    Helixi45 – 539Combined sources
    Beta strandi57 – 659Combined sources
    Helixi69 – 7810Combined sources
    Beta strandi82 – 876Combined sources
    Helixi92 – 10413Combined sources
    Beta strandi108 – 1136Combined sources
    Helixi119 – 1279Combined sources
    Beta strandi132 – 1365Combined sources
    Helixi139 – 1435Combined sources
    Helixi150 – 16112Combined sources
    Beta strandi165 – 1717Combined sources
    Helixi174 – 1807Combined sources
    Beta strandi186 – 1916Combined sources
    Helixi192 – 1954Combined sources
    Beta strandi197 – 1993Combined sources
    Helixi200 – 21415Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 2-216.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP39304.

    Family & Domainsi

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0269.
    HOGENOMiHOG000226068.
    InParanoidiP39304.
    KOiK03078.
    OMAiTIPTMKA.
    OrthoDBiEOG66B435.
    PhylomeDBiP39304.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01267. UlaD.
    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.

    Genome annotation databases

    EnsemblBacteriaiAAC77153; AAC77153; b4196.
    BAE78197; BAE78197; BAE78197.
    GeneIDi948714.
    KEGGiecj:Y75_p4082.
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 2-216.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-10869N.
    IntActiP39304. 1 interaction.
    STRINGi511145.b4196.

    2D gel databases

    SWISS-2DPAGEP39304.

    Proteomic databases

    PRIDEiP39304.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77153; AAC77153; b4196.
    BAE78197; BAE78197; BAE78197.
    GeneIDi948714.
    KEGGiecj:Y75_p4082.
    eco:b4196.
    PATRICi32123967. VBIEscCol129921_4328.

    Organism-specific databases

    EchoBASEiEB2389.
    EcoGeneiEG12496. ulaD.

    Phylogenomic databases

    eggNOGiCOG0269.
    HOGENOMiHOG000226068.
    InParanoidiP39304.
    KOiK03078.
    OMAiTIPTMKA.
    OrthoDBiEOG66B435.
    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.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    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. "Novel phosphotransferases system genes revealed by bacterial genome analysis: operons encoding homologues of sugar-specific permease domains of the phosphotransferase system and pentose catabolic enzymes."
      Reizer J., Charbit A., Reizer A., Saier M.H. Jr.
      Genome Sci. Technol. 1:53-75(1996)
      Cited for: DISCUSSION OF SEQUENCE.
    5. "Is the ribulose monophosphate pathway widely distributed in bacteria?"
      Reizer J., Reizer A., Saier M.H. Jr.
      Microbiology 143:2519-2520(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISCUSSION OF SEQUENCE.
    6. "Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons."
      Yew W.S., Gerlt J.A.
      J. Bacteriol. 184:302-306(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ROLE IN L-ASCORBATE UTILIZATION.
      Strain: K12 / MG1655 / ATCC 47076.
    7. "The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), which is involved in L-ascorbate metabolism in Escherichia coli."
      Campos E., Aguilar J., Baldoma L., Badia J.
      J. Bacteriol. 184:6065-6068(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: TRANSCRIPTIONAL REGULATION.
    8. "Regulation of expression of the divergent ulaG and ulaABCDEF operons involved in L-ascorbate dissimilation in Escherichia coli."
      Campos E., Baldoma L., Aguilar J., Badia J.
      J. Bacteriol. 186:1720-1728(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: TRANSCRIPTIONAL REGULATION.
    9. "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase."
      Yew W.S., Wise E.L., Rayment I., Gerlt J.A.
      Biochemistry 43:6427-6437(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF GLU-33; LYS-64; ASP-67; GLU-112; HIS-136 AND ARG-139, KINETIC PARAMETERS, REACTION STEREOCHEMISTRY.
    10. "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase."
      Yew W.S., Akana J., Wise E.L., Rayment I., Gerlt J.A.
      Biochemistry 44:1807-1815(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS.
    11. "Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase."
      Wise E., Yew W.S., Babbitt P.C., Gerlt J.A., Rayment I.
      Biochemistry 41:3861-3869(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS) OF COMPLEXES WITH MAGNESIUM; PHOSPHATE AND L-GULONATE-6-PHOSPHATE, SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.
    12. "Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily."
      Wise E.L., Yew W.S., Gerlt J.A., Rayment I.
      Biochemistry 42:12133-12142(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF COMPLEXES WITH L-GULONATE 6-PHOSPHATE; L-THREONOHYDROXAMATE 4-PHOSPHATE; L-XYLITOL 5-PHOSPHATE AND L-XYLULOSE 5-PHOSPHATE.
      Strain: K12 / MG1655 / ATCC 47076.
    13. "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase."
      Wise E.L., Yew W.S., Gerlt J.A., Rayment I.
      Biochemistry 43:6438-6446(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANTS ALA-64; ALA-136; GLN-112 AND GLN-112/ALA-136 IN COMPLEX WITH L-THREONOHYDROXAMATE 4-PHOSPHATE, REACTION MECHANISM.
    14. "Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase."
      Wise E.L., Yew W.S., Akana J., Gerlt J.A., Rayment I.
      Biochemistry 44:1816-1823(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF NATIVE PROTEIN IN COMPLEX WITH D-RIBULOSE 5-PHOSPHATE; MUTANTS ASP-112/ALA-169 AND ASP-11/VAL-139/ALA-169 IN COMPLEX WITH D-RIBULOSE 5-PHOSPHATE AND MUTANT ASP-11/VAL-139/ALA-169 IN COMPLEX WITH L-XYLULOSE 5-PHOSPHATE.

    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: June 24, 2015
    This is version 127 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

    External Data

    Dasty 3

    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 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.