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P39304

- ULAD_ECOLI

UniProt

P39304 - ULAD_ECOLI

Protein

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

Gene

ulaD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 121 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    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

    Binds 1 magnesium ion per subunit.

    Kineticsi

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

    Pathwayi

    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

    1. 3-dehydro-L-gulonate-6-phosphate decarboxylase activity Source: EcoCyc
    2. magnesium ion binding Source: EcoCyc
    3. orotidine-5'-phosphate decarboxylase activity Source: InterPro

    GO - Biological processi

    1. 'de novo' pyrimidine nucleobase biosynthetic process Source: InterPro
    2. L-ascorbic acid catabolic process Source: EcoCyc

    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.
    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG12496. ulaD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi33 – 331E → K: Loss of activity. 2 Publications
    Mutagenesisi64 – 641K → A: 16% of wild-type activity. 2 Publications
    Mutagenesisi67 – 671D → A: 5% of wild-type activity. 2 Publications
    Mutagenesisi112 – 1121E → A: 0.5% of wild-type activity. 2 Publications
    Mutagenesisi136 – 1361H → A: 5% of wild-type activity. 2 Publications
    Mutagenesisi139 – 1391R → V: 17% of wild-type activity. 2 Publications

    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

    Gene expression databases

    GenevestigatoriP39304.

    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 – 106
    Helixi15 – 2511
    Helixi26 – 283
    Beta strandi30 – 345
    Helixi36 – 427
    Helixi45 – 539
    Beta strandi57 – 659
    Helixi69 – 7810
    Beta strandi82 – 876
    Helixi92 – 10413
    Beta strandi108 – 1136
    Helixi119 – 1279
    Beta strandi132 – 1365
    Helixi139 – 1435
    Helixi150 – 16112
    Beta strandi165 – 1717
    Helixi174 – 1807
    Beta strandi186 – 1916
    Helixi192 – 1954
    Beta strandi197 – 1993
    Helixi200 – 21415

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK03078.
    OMAiSHAYETT.
    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

    MSLPMLQVAL DNQTMDSAYE TTRLIAEEVD IIEVGTILCV GEGVRAVRDL    50
    KALYPHKIVL ADAKIADAGK ILSRMCFEAN ADWVTVICCA DINTAKGALD 100
    VAKEFNGDVQ IELTGYWTWE QAQQWRDAGI GQVVYHRSRD AQAAGVAWGE 150
    ADITAIKRLS DMGFKVTVTG GLALEDLPLF KGIPIHVFIA GRSIRDAASP 200
    VEAARQFKRS IAELWG 216
    Length:216
    Mass (Da):23,578
    Last modified:February 1, 1995 - v1
    Checksum:iEC8490DA1D02D824
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_492338.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77153; AAC77153; b4196.
    BAE78197; BAE78197; BAE78197.
    GeneIDi12933006.
    948714.
    KEGGiecj:Y75_p4082.
    eco:b4196.
    PATRICi32123967. VBIEscCol129921_4328.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U14003 Genomic DNA. Translation: AAA97092.1 .
    U00096 Genomic DNA. Translation: AAC77153.1 .
    AP009048 Genomic DNA. Translation: BAE78197.1 .
    PIRi S56421.
    RefSeqi NP_418617.1. NC_000913.3.
    YP_492338.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1KV8 X-ray 1.62 A/B 1-216 [» ]
    1KW1 X-ray 2.20 A/B 1-216 [» ]
    1Q6L X-ray 1.80 A/B 1-216 [» ]
    1Q6O X-ray 1.20 A/B 1-216 [» ]
    1Q6Q X-ray 1.70 A/B 1-216 [» ]
    1Q6R X-ray 1.76 A/B 1-216 [» ]
    1SO3 X-ray 1.90 A/B 1-216 [» ]
    1SO4 X-ray 1.70 A/B 1-216 [» ]
    1SO5 X-ray 1.80 A/B 1-216 [» ]
    1SO6 X-ray 1.90 A/B 1-216 [» ]
    1XBV X-ray 1.66 A/B 1-216 [» ]
    1XBX X-ray 1.81 A/B 1-216 [» ]
    1XBY X-ray 1.58 A/B 1-216 [» ]
    1XBZ X-ray 1.80 A/B 1-216 [» ]
    ProteinModelPortali P39304.
    SMRi P39304. Positions 2-216.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10869N.
    IntActi P39304. 1 interaction.
    STRINGi 511145.b4196.

    2D gel databases

    SWISS-2DPAGE P39304.

    Proteomic databases

    PRIDEi P39304.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC77153 ; AAC77153 ; b4196 .
    BAE78197 ; BAE78197 ; BAE78197 .
    GeneIDi 12933006.
    948714.
    KEGGi ecj:Y75_p4082.
    eco:b4196.
    PATRICi 32123967. VBIEscCol129921_4328.

    Organism-specific databases

    EchoBASEi EB2389.
    EcoGenei EG12496. ulaD.

    Phylogenomic databases

    eggNOGi COG0269.
    HOGENOMi HOG000226068.
    KOi K03078.
    OMAi SHAYETT.
    OrthoDBi EOG66B435.
    PhylomeDBi P39304.

    Enzyme and pathway databases

    UniPathwayi UPA00263 ; UER00378 .
    BioCyci EcoCyc:G7858-MONOMER.
    ECOL316407:JW4154-MONOMER.
    MetaCyc:G7858-MONOMER.
    SABIO-RK P39304.

    Miscellaneous databases

    EvolutionaryTracei P39304.
    PROi P39304.

    Gene expression databases

    Genevestigatori P39304.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_01267. UlaD.
    InterProi IPR023942. 3-keto-L-gulonate6Pdecase_UlaD.
    IPR013785. Aldolase_TIM.
    IPR001754. OMPdeCOase_dom.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view ]
    Pfami PF00215. OMPdecase. 1 hit.
    [Graphical view ]
    SMARTi SM00934. OMPdecase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51366. SSF51366. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 121 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