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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

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. carbohydrate metabolic process Source: TAIR
  2. cell wall pectin metabolic process Source: TAIR
  3. 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

  1. cytosol Source: TAIR
  2. 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

Gene expression databases

GenevestigatoriQ9LIA8.

Interactioni

Protein-protein interaction databases

BioGridi7923. 1 interaction.
IntActiQ9LIA8. 1 interaction.

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.

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.

Gene expression databases

GenevestigatoriQ9LIA8.

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: April 29, 2015
This is version 118 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.