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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

Pathwayi

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

  1. NAD binding Source: InterPro
  2. UDP-glucose 6-dehydrogenase activity Source: UniProtKB

GO - Biological processi

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

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciARA:AT5G39320-MONOMER.
ReactomeiREACT_248754. 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: Chromosome 5

Organism-specific databases

TAIRiAT5G39320.

Subcellular locationi

GO - Cellular componenti

  1. apoplast Source: TAIR
  2. cytosol Source: TAIR
  3. 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

Gene expression databases

GenevestigatoriQ9FM01.

Interactioni

Protein-protein interaction databases

BioGridi19179. 1 interaction.
IntActiQ9FM01. 1 interaction.

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.
OMAiTTIAIND.
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.

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.
OMAiTTIAIND.
PhylomeDBiQ9FM01.

Enzyme and pathway databases

UniPathwayiUPA00038; UER00491.
BioCyciARA:AT5G39320-MONOMER.
ReactomeiREACT_248754. Formation of the active cofactor, UDP-glucuronate.

Gene expression databases

GenevestigatoriQ9FM01.

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: February 4, 2015
This is version 103 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.