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Protein

UDP-glucose 6-dehydrogenase 2

Gene

UGD2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers. Required for the formation of cell wall ingrowths on the outer cell walls of nematode-induced syncytia.3 Publications

Catalytic activityi

UDP-glucose + 2 NAD+ + H2O = UDP-glucuronate + 2 NADH.

Enzyme regulationi

Inhibited by UDP-xylose.1 Publication

Kineticsi

  1. KM=43 µM for NAD+1 Publication
  2. KM=123 µM for UDP-glucose1 Publication

    Pathway: UDP-alpha-D-glucuronate biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes UDP-alpha-D-glucuronate from UDP-alpha-D-glucose.
    Proteins known to be involved in this subpathway in this organism are:
    1. UDP-glucose 6-dehydrogenase 2 (UGD2), UDP-glucose 6-dehydrogenase 1 (UGD1), UDP-glucose 6-dehydrogenase 4 (UGD4), UDP-glucose 6-dehydrogenase 3 (UGD3)
    This subpathway is part of the pathway UDP-alpha-D-glucuronate biosynthesis, which is itself part of Nucleotide-sugar biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes UDP-alpha-D-glucuronate from UDP-alpha-D-glucose, the pathway UDP-alpha-D-glucuronate biosynthesis and in Nucleotide-sugar biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei33 – 331NADBy similarity
    Binding sitei38 – 381NADBy similarity
    Binding sitei161 – 1611NADBy similarity
    Active sitei272 – 2721NucleophileBy similarity
    Binding sitei342 – 3421NADBy similarity
    Binding sitei447 – 4471SubstrateBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi8 – 136NADBy similarity
    Nucleotide bindingi86 – 905NADBy similarity
    Nucleotide bindingi127 – 1282NADBy similarity
    Nucleotide bindingi272 – 2754NADBy similarity

    GO - Molecular functioni

    • NAD binding Source: InterPro
    • UDP-glucose 6-dehydrogenase activity Source: UniProtKB

    GO - Biological processi

    • carbohydrate metabolic process Source: TAIR
    • cell wall pectin metabolic process Source: TAIR
    • UDP-glucuronate biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciARA:AT3G29360-MONOMER.
    ARA:GQT-2548-MONOMER.
    BRENDAi1.1.1.22. 399.
    ReactomeiREACT_310241. Formation of the active cofactor, UDP-glucuronate.
    UniPathwayiUPA00038; UER00491.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    UDP-glucose 6-dehydrogenase 2 (EC:1.1.1.22)
    Short name:
    UDP-Glc dehydrogenase 2
    Short name:
    UDP-GlcDH 2
    Short name:
    UDPGDH 2
    Alternative name(s):
    At-UGD2
    Gene namesi
    Name:UGD2
    Synonyms:UGD
    Ordered Locus Names:At3g29360
    ORF Names:MUO10.18, MUO10_6
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548 Componenti: Chromosome 3

    Organism-specific databases

    TAIRiAT3G29360.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: TAIR
    • nucleus Source: TAIR
    Complete GO annotation...

    Pathology & Biotechi

    Disruption phenotypei

    No visible phenotype. Displays smaller nematode-induced syncytia. The UGD2 UGD3 double mutant displays a strong dwarf phenotype and often develops seedlings with severe root defects; cell walls have an altered sugar composition (PubMed:21949134). Ugd2 and ugd3 double mutants display abnormal nematode-induced syncytia (PubMed:22848518).2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 480480UDP-glucose 6-dehydrogenase 2PRO_0000312027Add
    BLAST

    Proteomic databases

    PaxDbiQ9LIA8.
    PRIDEiQ9LIA8.

    Expressioni

    Tissue specificityi

    Preferentially expressed in roots.1 Publication

    Developmental stagei

    Restricted expression to the primary root in young seedlings. Later detected in hypocotyl, leaves but with the strongest expression in the root system.2 Publications

    Interactioni

    Protein-protein interaction databases

    BioGridi7923. 1 interaction.
    IntActiQ9LIA8. 1 interaction.
    STRINGi3702.AT3G29360.1.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9LIA8.
    SMRiQ9LIA8. Positions 3-467.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni157 – 1615Substrate bindingBy similarity
    Regioni216 – 2238Substrate bindingBy similarity
    Regioni256 – 26914Substrate bindingBy similarityAdd
    BLAST
    Regioni334 – 3352Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1004.
    HOGENOMiHOG000153773.
    InParanoidiQ9LIA8.
    KOiK00012.
    OMAiRNIMNLQ.
    PhylomeDBiQ9LIA8.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    InterProiIPR008927. 6-PGluconate_DH_C-like.
    IPR016040. NAD(P)-bd_dom.
    IPR017476. UDP-Glc/GDP-Man.
    IPR014027. UDP-Glc/GDP-Man_DH_C.
    IPR014026. UDP-Glc/GDP-Man_DH_dimer.
    IPR001732. UDP-Glc/GDP-Man_DH_N.
    IPR028356. UDPglc_DH_euk.
    [Graphical view]
    PANTHERiPTHR11374. PTHR11374. 1 hit.
    PTHR11374:SF3. PTHR11374:SF3. 1 hit.
    PfamiPF00984. UDPG_MGDP_dh. 1 hit.
    PF03720. UDPG_MGDP_dh_C. 1 hit.
    PF03721. UDPG_MGDP_dh_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF500133. UDPglc_DH_euk. 1 hit.
    PIRSF000124. UDPglc_GDPman_dh. 1 hit.
    SMARTiSM00984. UDPG_MGDP_dh_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF52413. SSF52413. 1 hit.
    TIGRFAMsiTIGR03026. NDP-sugDHase. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9LIA8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVKICCIGAG YVGGPTMAVI ALKCPDVEVA VVDISVPRIN AWNSDTLPIY
    60 70 80 90 100
    EPGLDDVVKQ CRGKNLFFST DVEKHVREAD IVFVSVNTPT KTRGLGAGKA
    110 120 130 140 150
    ADLTYWESAA RMIADVSVSD KIVVEKSTVP VKTAEAIEKI LTHNSKGIKF
    160 170 180 190 200
    QILSNPEFLA EGTAIKDLFN PDRVLIGGRE TPEGFKAVQT LKNVYAHWVP
    210 220 230 240 250
    EGQIITTNLW SAELSKLAAN AFLAQRISSV NAMSALCEAT GADVTQVSYA
    260 270 280 290 300
    VGTDSRIGPK FLNSSVGFGG SCFQKDILNL VYICECNGLP EVAEYWKQVI
    310 320 330 340 350
    KINDYQKSRF VNRVVSSMFN SVSNKKIAVL GFAFKKDTGD TRETPAIDVC
    360 370 380 390 400
    KGLLEDKARL SIYDPQVTED QIQRDLSMNK FDWDHPLHLQ PMSPTTVKQV
    410 420 430 440 450
    TVTWDAYEAT KDAHGICIMT EWDEFKNLDF QKIFDNMQKP AFVFDGRNIM
    460 470 480
    NLQKLREIGF IVYSIGKPLD DWLKDMPAVA
    Length:480
    Mass (Da):53,173
    Last modified:October 1, 2000 - v1
    Checksum:iD6281D20442CBADF
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti12 – 121V → I in AAL11570 (PubMed:14593172).Curated
    Sequence conflicti178 – 1781G → R in AAL11570 (PubMed:14593172).Curated
    Sequence conflicti193 – 1931N → D in AAM67208 (Ref. 7) Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP001309 Genomic DNA. Translation: BAB02581.1.
    CP002686 Genomic DNA. Translation: AEE77573.1.
    CP002686 Genomic DNA. Translation: AEE77574.1.
    AF424576 mRNA. Translation: AAL11570.1.
    BT021126 mRNA. Translation: AAX22261.1.
    AK226539 mRNA. Translation: BAE98678.1.
    BT029164 mRNA. Translation: ABJ17099.1.
    AY088902 mRNA. Translation: AAM67208.1.
    RefSeqiNP_001030792.1. NM_001035715.1.
    NP_189582.1. NM_113861.3.
    UniGeneiAt.22975.

    Genome annotation databases

    EnsemblPlantsiAT3G29360.1; AT3G29360.1; AT3G29360.
    AT3G29360.2; AT3G29360.2; AT3G29360.
    GeneIDi822594.
    KEGGiath:AT3G29360.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AP001309 Genomic DNA. Translation: BAB02581.1.
    CP002686 Genomic DNA. Translation: AEE77573.1.
    CP002686 Genomic DNA. Translation: AEE77574.1.
    AF424576 mRNA. Translation: AAL11570.1.
    BT021126 mRNA. Translation: AAX22261.1.
    AK226539 mRNA. Translation: BAE98678.1.
    BT029164 mRNA. Translation: ABJ17099.1.
    AY088902 mRNA. Translation: AAM67208.1.
    RefSeqiNP_001030792.1. NM_001035715.1.
    NP_189582.1. NM_113861.3.
    UniGeneiAt.22975.

    3D structure databases

    ProteinModelPortaliQ9LIA8.
    SMRiQ9LIA8. Positions 3-467.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi7923. 1 interaction.
    IntActiQ9LIA8. 1 interaction.
    STRINGi3702.AT3G29360.1.

    Proteomic databases

    PaxDbiQ9LIA8.
    PRIDEiQ9LIA8.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT3G29360.1; AT3G29360.1; AT3G29360.
    AT3G29360.2; AT3G29360.2; AT3G29360.
    GeneIDi822594.
    KEGGiath:AT3G29360.

    Organism-specific databases

    TAIRiAT3G29360.

    Phylogenomic databases

    eggNOGiCOG1004.
    HOGENOMiHOG000153773.
    InParanoidiQ9LIA8.
    KOiK00012.
    OMAiRNIMNLQ.
    PhylomeDBiQ9LIA8.

    Enzyme and pathway databases

    UniPathwayiUPA00038; UER00491.
    BioCyciARA:AT3G29360-MONOMER.
    ARA:GQT-2548-MONOMER.
    BRENDAi1.1.1.22. 399.
    ReactomeiREACT_310241. Formation of the active cofactor, UDP-glucuronate.

    Miscellaneous databases

    PROiQ9LIA8.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    InterProiIPR008927. 6-PGluconate_DH_C-like.
    IPR016040. NAD(P)-bd_dom.
    IPR017476. UDP-Glc/GDP-Man.
    IPR014027. UDP-Glc/GDP-Man_DH_C.
    IPR014026. UDP-Glc/GDP-Man_DH_dimer.
    IPR001732. UDP-Glc/GDP-Man_DH_N.
    IPR028356. UDPglc_DH_euk.
    [Graphical view]
    PANTHERiPTHR11374. PTHR11374. 1 hit.
    PTHR11374:SF3. PTHR11374:SF3. 1 hit.
    PfamiPF00984. UDPG_MGDP_dh. 1 hit.
    PF03720. UDPG_MGDP_dh_C. 1 hit.
    PF03721. UDPG_MGDP_dh_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF500133. UDPglc_DH_euk. 1 hit.
    PIRSF000124. UDPglc_GDPman_dh. 1 hit.
    SMARTiSM00984. UDPG_MGDP_dh_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF52413. SSF52413. 1 hit.
    TIGRFAMsiTIGR03026. NDP-sugDHase. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones."
      Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.
      DNA Res. 7:217-221(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    4. "Arabidopsis ORF clones."
      Cheuk R.F., Chen H., Kim C.J., Shinn P., Ecker J.R.
      Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    6. "Arabidopsis ORF Clone."
      Bautista V.R., Kim C.J., Chen H., Quinitio C., Ecker J.R.
      Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    7. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    8. "Matrix polysaccharide precursors in Arabidopsis cell walls are synthesized by alternate pathways with organ-specific expression patterns."
      Seitz B., Klos C., Wurm M., Tenhaken R.
      Plant J. 21:537-546(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    9. "Molecular genetics of nucleotide sugar interconversion pathways in plants."
      Reiter W.-D., Vanzin G.F.
      Plant Mol. Biol. 47:95-113(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY.
    10. "Nucleotide sugar interconversions and cell wall biosynthesis: how to bring the inside to the outside."
      Seifert G.J.
      Curr. Opin. Plant Biol. 7:277-284(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    11. "Genome-wide analysis of the UDP-glucose dehydrogenase gene family in Arabidopsis, a key enzyme for matrix polysaccharides in cell walls."
      Klinghammer M., Tenhaken R.
      J. Exp. Bot. 58:3609-3621(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY, NOMENCLATURE, DEVELOPMENTAL STAGE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
    12. "Down-regulation of UDP-glucuronic acid biosynthesis leads to swollen plant cell walls and severe developmental defects associated with changes in pectic polysaccharides."
      Reboul R., Geserick C., Pabst M., Frey B., Wittmann D., Luetz-Meindl U., Leonard R., Tenhaken R.
      J. Biol. Chem. 286:39982-39992(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE, FUNCTION.
    13. "Cell wall ingrowths in nematode induced syncytia require UGD2 and UGD3."
      Siddique S., Sobczak M., Tenhaken R., Grundler F.M., Bohlmann H.
      PLoS ONE 7:E41515-E41515(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE, FUNCTION.

    Entry informationi

    Entry nameiUGDH2_ARATH
    AccessioniPrimary (citable) accession number: Q9LIA8
    Secondary accession number(s): Q8L8N1, Q944R8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 4, 2007
    Last sequence update: October 1, 2000
    Last modified: June 24, 2015
    This is version 119 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. 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.