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Protein

UDP-glucose 6-dehydrogenase 4

Gene

UGD4

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.

Catalytic activityi

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

Enzyme regulationi

Inhibited by UDP-xylose.1 Publication

Kineticsi

  1. KM=44 µM for NAD+1 Publication
  2. KM=171 µM for UDP-glucose1 Publication

    Pathway:iUDP-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

    • UDP-glucuronate biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciARA:AT5G39320-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 4 (EC:1.1.1.22)
    Short name:
    UDP-Glc dehydrogenase 4
    Short name:
    UDP-GlcDH 4
    Short name:
    UDPGDH 4
    Alternative name(s):
    At-UGD4
    Gene namesi
    Name:UGD4
    Synonyms:UGD1
    Ordered Locus Names:At5g39320
    ORF Names:K3K3.170
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548 Componenti: Chromosome 5

    Organism-specific databases

    TAIRiAT5G39320.

    Subcellular locationi

    GO - Cellular componenti

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

    Pathology & Biotechi

    Disruption phenotypei

    No visible phenotype.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 480480UDP-glucose 6-dehydrogenase 4PRO_0000312028Add
    BLAST

    Proteomic databases

    PaxDbiQ9FM01.
    PRIDEiQ9FM01.

    Expressioni

    Developmental stagei

    Restricted expression to the primary root in young seedlings. Later detected in hypocotyl, leaves and flowers.1 Publication

    Inductioni

    Specifically down-regulated by H.schachtii (cyst nematodes) in nematode-induced syncytia.1 Publication

    Interactioni

    Protein-protein interaction databases

    BioGridi19179. 1 interaction.
    IntActiQ9FM01. 1 interaction.
    STRINGi3702.AT5G39320.1.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9FM01.
    SMRiQ9FM01. 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.
    InParanoidiQ9FM01.
    KOiK00012.
    OMAiGRNIMNV.
    PhylomeDBiQ9FM01.

    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.

    Q9FM01-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MVKICCIGAG YVGGPTMAVI ALKCPDIEVA VVDISVPRIN AWNSDQLPIY
    60 70 80 90 100
    EPGLDDIVKQ CRGKNLFFST DVEKHVREAD IVFVSVNTPT KTTGLGAGKA
    110 120 130 140 150
    ADLTYWESAA RMIADVSVSD KIVVEKSTVP VKTAEAIEKI LMHNSKGIKF
    160 170 180 190 200
    QILSNPEFLA EGTAIADLFN PDRVLIGGRE TPEGFKAVQT LKEVYANWVP
    210 220 230 240 250
    EGQIITTNLW SAELSKLAAN AFLAQRISSV NAMSALCEST GADVTQVSYA
    260 270 280 290 300
    VGTDSRIGSK FLNASVGFGG SCFQKDILNL VYICQCNGLP EVAEYWKQVI
    310 320 330 340 350
    KINDYQKNRF VNRIVSSMFN TVSNKKVAIL GFAFKKDTGD TRETPAIDVC
    360 370 380 390 400
    KGLLGDKAQI SIYDPQVTEE QIQRDLSMKK FDWDHPLHLQ PMSPTTVKQV
    410 420 430 440 450
    SVTWDAYEAT KDAHAVCVLT EWDEFKSLDY QKIFDNMQKP AFIFDGRNIM
    460 470 480
    NVNKLREIGF IVYSIGKPLD PWLKDMPAFV
    Length:480
    Mass (Da):53,097
    Last modified:March 1, 2001 - v1
    Checksum:i3FC4FEB2CB647BCB
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti92 – 921Missing in AAP21188 (PubMed:14593172).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB009054, AB010694 Genomic DNA. Translation: BAB11006.1.
    CP002688 Genomic DNA. Translation: AED94419.1.
    BT006380 mRNA. Translation: AAP21188.1.
    RefSeqiNP_198748.1. NM_123294.3.
    UniGeneiAt.20102.
    At.71506.

    Genome annotation databases

    EnsemblPlantsiAT5G39320.1; AT5G39320.1; AT5G39320.
    GeneIDi833928.
    KEGGiath:AT5G39320.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB009054, AB010694 Genomic DNA. Translation: BAB11006.1.
    CP002688 Genomic DNA. Translation: AED94419.1.
    BT006380 mRNA. Translation: AAP21188.1.
    RefSeqiNP_198748.1. NM_123294.3.
    UniGeneiAt.20102.
    At.71506.

    3D structure databases

    ProteinModelPortaliQ9FM01.
    SMRiQ9FM01. Positions 3-467.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi19179. 1 interaction.
    IntActiQ9FM01. 1 interaction.
    STRINGi3702.AT5G39320.1.

    Proteomic databases

    PaxDbiQ9FM01.
    PRIDEiQ9FM01.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT5G39320.1; AT5G39320.1; AT5G39320.
    GeneIDi833928.
    KEGGiath:AT5G39320.

    Organism-specific databases

    TAIRiAT5G39320.

    Phylogenomic databases

    eggNOGiCOG1004.
    HOGENOMiHOG000153773.
    InParanoidiQ9FM01.
    KOiK00012.
    OMAiGRNIMNV.
    PhylomeDBiQ9FM01.

    Enzyme and pathway databases

    UniPathwayiUPA00038; UER00491.
    BioCyciARA:AT5G39320-MONOMER.
    BRENDAi1.1.1.22. 399.
    ReactomeiREACT_310241. Formation of the active cofactor, UDP-glucuronate.

    Miscellaneous databases

    PROiQ9FM01.

    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 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones."
      Sato S., Kaneko T., Kotani H., Nakamura Y., Asamizu E., Miyajima N., Tabata S.
      DNA Res. 5:41-54(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones."
      Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N., Tabata S.
      DNA Res. 5:131-145(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "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.
    5. "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.
    6. "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.
    7. "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.
    8. "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, INDUCTION.

    Entry informationi

    Entry nameiUGDH4_ARATH
    AccessioniPrimary (citable) accession number: Q9FM01
    Secondary accession number(s): Q84MD5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 4, 2007
    Last sequence update: March 1, 2001
    Last modified: July 22, 2015
    This is version 107 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally assigned as UGD1.1 Publication

    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.