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Protein

UDP-glucose 6-dehydrogenase

Gene

sqv-4

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of glycosaminoglycans; hyaluronan, chondroitin sulfate, and heparan sulfate.1 Publication

Catalytic activityi

UDP-glucose + 2 NAD+ + H2O = UDP-glucuronate + 2 NADH.1 Publication

Kineticsi

  1. KM=0.2 mM for UDP-glucose at 22 degrees Celsius1 Publication
  2. KM=0.2 mM for NAD+at 22 degrees Celsius1 Publication

    Pathwayi: 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.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. UDP-glucose 6-dehydrogenase (sqv-4)
    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)DescriptionActionsGraphical viewLength
    Binding sitei41NADBy similarity1
    Binding sitei46NADBy similarity1
    Binding sitei172NADBy similarity1
    Binding sitei267SubstrateBy similarity1
    Active sitei283NucleophileBy similarity1
    Binding sitei353NADBy similarity1
    Binding sitei447SubstrateBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi16 – 21NADBy similarity6
    Nucleotide bindingi94 – 98NADBy similarity5
    Nucleotide bindingi135 – 136NADBy similarity2
    Nucleotide bindingi283 – 286NADBy similarity4

    GO - Molecular functioni

    • identical protein binding Source: IntAct
    • NAD binding Source: InterPro
    • UDP-glucose 6-dehydrogenase activity Source: WormBase

    GO - Biological processi

    • embryo development ending in birth or egg hatching Source: WormBase
    • glycosaminoglycan biosynthetic process Source: WormBase
    • morphogenesis of an epithelium Source: WormBase
    • oviposition Source: WormBase
    • reproduction Source: WormBase
    • UDP-glucuronate biosynthetic process Source: UniProtKB-UniPathway
    • vulval development Source: WormBase

    Keywordsi

    Molecular functionOxidoreductase
    LigandNAD

    Enzyme and pathway databases

    BRENDAi1.1.1.22. 1045.
    ReactomeiR-CEL-173599. Formation of the active cofactor, UDP-glucuronate.
    UniPathwayiUPA00038; UER00491.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    UDP-glucose 6-dehydrogenase (EC:1.1.1.221 Publication)
    Short name:
    UDP-Glc dehydrogenase
    Short name:
    UDP-GlcDH
    Short name:
    UDPGDH
    Alternative name(s):
    Squashed vulva protein 4
    Gene namesi
    Name:sqv-4
    ORF Names:F29F11.1
    OrganismiCaenorhabditis elegans
    Taxonomic identifieri6239 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
    Proteomesi
    • UP000001940 Componenti: Chromosome V

    Organism-specific databases

    WormBaseiF29F11.1; CE05767; WBGene00005022; sqv-4.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: WormBase

    Pathology & Biotechi

    Disruption phenotypei

    RNAi-mediated knockdown causes a reduction in the size of cortical granules during the first meiotic division.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi353R → H in n2827; defects in vulva morphogenesis during L4 larval stage. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000740631 – 481UDP-glucose 6-dehydrogenaseAdd BLAST481

    Proteomic databases

    EPDiQ19905.
    PaxDbiQ19905.
    PeptideAtlasiQ19905.
    PRIDEiQ19905.

    Expressioni

    Tissue specificityi

    Expressed in the vulva and in oocytes.1 Publication

    Developmental stagei

    Expression increases in a subset of vulva precursor cells during middle and late L4 larval stage.1 Publication

    Gene expression databases

    BgeeiWBGene00005022.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-320696,EBI-320696

    GO - Molecular functioni

    • identical protein binding Source: IntAct

    Protein-protein interaction databases

    BioGridi44513. 6 interactors.
    DIPiDIP-24290N.
    IntActiQ19905. 18 interactors.
    MINTiMINT-1063665.
    STRINGi6239.F29F11.1.2.

    Structurei

    Secondary structure

    1481
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi11 – 15Combined sources5
    Helixi21 – 31Combined sources11
    Beta strandi35 – 40Combined sources6
    Helixi44 – 50Combined sources7
    Beta strandi52 – 54Combined sources3
    Helixi62 – 69Combined sources8
    Turni71 – 73Combined sources3
    Beta strandi74 – 78Combined sources5
    Helixi80 – 86Combined sources7
    Beta strandi88 – 92Combined sources5
    Turni103 – 107Combined sources5
    Helixi112 – 124Combined sources13
    Beta strandi129 – 133Combined sources5
    Helixi141 – 152Combined sources12
    Beta strandi161 – 165Combined sources5
    Helixi175 – 180Combined sources6
    Beta strandi185 – 189Combined sources5
    Helixi193 – 207Combined sources15
    Helixi212 – 214Combined sources3
    Beta strandi215 – 219Combined sources5
    Helixi220 – 251Combined sources32
    Helixi255 – 263Combined sources9
    Turni266 – 268Combined sources3
    Beta strandi270 – 272Combined sources3
    Beta strandi281 – 283Combined sources3
    Helixi284 – 297Combined sources14
    Helixi301 – 328Combined sources28
    Turni329 – 331Combined sources3
    Beta strandi337 – 341Combined sources5
    Beta strandi344 – 346Combined sources3
    Helixi356 – 366Combined sources11
    Beta strandi370 – 374Combined sources5
    Beta strandi376 – 378Combined sources3
    Helixi380 – 390Combined sources11
    Helixi393 – 399Combined sources7
    Beta strandi400 – 405Combined sources6
    Helixi406 – 410Combined sources5
    Beta strandi414 – 418Combined sources5
    Helixi423 – 425Combined sources3
    Helixi430 – 436Combined sources7
    Beta strandi442 – 448Combined sources7
    Helixi452 – 458Combined sources7
    Beta strandi461 – 464Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2O3JX-ray1.88A/B/C1-481[»]
    ProteinModelPortaliQ19905.
    SMRiQ19905.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ19905.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni168 – 172Substrate bindingBy similarity5
    Regioni227 – 231Substrate bindingBy similarity5
    Regioni274 – 280Substrate bindingBy similarity7
    Regioni345 – 346Substrate bindingBy similarity2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG2666. Eukaryota.
    COG1004. LUCA.
    GeneTreeiENSGT00390000015355.
    HOGENOMiHOG000153773.
    InParanoidiQ19905.
    KOiK00012.
    OMAiLCTEWDE.
    OrthoDBiEOG091G05RK.
    PhylomeDBiQ19905.

    Family and domain databases

    InterProiView protein in InterPro
    IPR008927. 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.
    PfamiView protein in Pfam
    PF00984. UDPG_MGDP_dh. 1 hit.
    PF03720. UDPG_MGDP_dh_C. 1 hit.
    PF03721. UDPG_MGDP_dh_N. 1 hit.
    PIRSFiPIRSF500133. UDPglc_DH_euk. 1 hit.
    PIRSF000124. UDPglc_GDPman_dh. 1 hit.
    SMARTiView protein in SMART
    SM00984. UDPG_MGDP_dh_C. 1 hit.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    SSF52413. SSF52413. 1 hit.
    TIGRFAMsiTIGR03026. NDP-sugDHase. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q19905-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTDQVFGKVS KVVCVGAGYV GGPTCAMIAH KCPHITVTVV DMNTAKIAEW
    60 70 80 90 100
    NSDKLPIYEP GLDEIVFAAR GRNLFFSSDI PKAIAEADLI FISVNTPTKM
    110 120 130 140 150
    YGRGKGMAPD LKYVESVSRT IAQYAGGPKI VVEKSTVPVK AAESIGCILR
    160 170 180 190 200
    EAQKNNENLK FQVLSNPEFL AEGTAMKDLA NPDRVLIGGE SSPEGLQAVA
    210 220 230 240 250
    ELVRIYENWV PRNRIITTNT WSSELSKLVA NAFLAQRISS INSISAVCEA
    260 270 280 290 300
    TGAEISEVAH AVGYDTRIGS KFLQASVGFG GSCFQKDVLS LVYLCESLNL
    310 320 330 340 350
    PQVADYWQGV ININNWQRRR FADKIIAELF NTVTDKKIAI FGFAFKKNTG
    360 370 380 390 400
    DTRESSAIHV IKHLMEEHAK LSVYDPKVQK SQMLNDLASV TSAQDVERLI
    410 420 430 440 450
    TVESDPYAAA RGAHAIVVLT EWDEFVELNY SQIHNDMQHP AAIFDGRLIL
    460 470 480
    DQKALREIGF RTFAIGTSPD QAYNLFGTAG Y
    Length:481
    Mass (Da):52,755
    Last modified:November 1, 1996 - v1
    Checksum:i4E789DC5D6679531
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY147932 mRNA. Translation: AAN39842.1.
    Z73974 Genomic DNA. Translation: CAA98269.1.
    PIRiT21550.
    RefSeqiNP_505730.1. NM_073329.7.
    UniGeneiCel.19769.

    Genome annotation databases

    EnsemblMetazoaiF29F11.1; F29F11.1; WBGene00005022.
    GeneIDi179484.
    KEGGicel:CELE_F29F11.1.
    UCSCiF29F11.1.1. c. elegans.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY147932 mRNA. Translation: AAN39842.1.
    Z73974 Genomic DNA. Translation: CAA98269.1.
    PIRiT21550.
    RefSeqiNP_505730.1. NM_073329.7.
    UniGeneiCel.19769.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2O3JX-ray1.88A/B/C1-481[»]
    ProteinModelPortaliQ19905.
    SMRiQ19905.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi44513. 6 interactors.
    DIPiDIP-24290N.
    IntActiQ19905. 18 interactors.
    MINTiMINT-1063665.
    STRINGi6239.F29F11.1.2.

    Proteomic databases

    EPDiQ19905.
    PaxDbiQ19905.
    PeptideAtlasiQ19905.
    PRIDEiQ19905.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblMetazoaiF29F11.1; F29F11.1; WBGene00005022.
    GeneIDi179484.
    KEGGicel:CELE_F29F11.1.
    UCSCiF29F11.1.1. c. elegans.

    Organism-specific databases

    CTDi179484.
    WormBaseiF29F11.1; CE05767; WBGene00005022; sqv-4.

    Phylogenomic databases

    eggNOGiKOG2666. Eukaryota.
    COG1004. LUCA.
    GeneTreeiENSGT00390000015355.
    HOGENOMiHOG000153773.
    InParanoidiQ19905.
    KOiK00012.
    OMAiLCTEWDE.
    OrthoDBiEOG091G05RK.
    PhylomeDBiQ19905.

    Enzyme and pathway databases

    UniPathwayiUPA00038; UER00491.
    BRENDAi1.1.1.22. 1045.
    ReactomeiR-CEL-173599. Formation of the active cofactor, UDP-glucuronate.

    Miscellaneous databases

    EvolutionaryTraceiQ19905.
    PROiPR:Q19905.

    Gene expression databases

    BgeeiWBGene00005022.

    Family and domain databases

    InterProiView protein in InterPro
    IPR008927. 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.
    PfamiView protein in Pfam
    PF00984. UDPG_MGDP_dh. 1 hit.
    PF03720. UDPG_MGDP_dh_C. 1 hit.
    PF03721. UDPG_MGDP_dh_N. 1 hit.
    PIRSFiPIRSF500133. UDPglc_DH_euk. 1 hit.
    PIRSF000124. UDPglc_GDPman_dh. 1 hit.
    SMARTiView protein in SMART
    SM00984. UDPG_MGDP_dh_C. 1 hit.
    SUPFAMiSSF48179. SSF48179. 1 hit.
    SSF51735. SSF51735. 1 hit.
    SSF52413. SSF52413. 1 hit.
    TIGRFAMsiTIGR03026. NDP-sugDHase. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiUGDH_CAEEL
    AccessioniPrimary (citable) accession number: Q19905
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: November 1, 1996
    Last modified: June 7, 2017
    This is version 131 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programCaenorhabditis annotation project

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Caenorhabditis elegans
      Caenorhabditis elegans: entries, gene names and cross-references to WormBase
    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.