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Q9FM01 (UGDH4_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 98. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
UDP-glucose 6-dehydrogenase 4

Short name=UDP-Glc dehydrogenase 4
Short name=UDP-GlcDH 4
Short name=UDPGDH 4
EC=1.1.1.22
Alternative name(s):
At-UGD4
Gene names
Name:UGD4
Synonyms:UGD1
Ordered Locus Names:At5g39320
ORF Names:K3K3.170
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length480 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers.

Catalytic activity

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

Enzyme regulation

Inhibited by UDP-xylose. Ref.7

Pathway

Nucleotide-sugar biosynthesis; UDP-alpha-D-glucuronate biosynthesis; UDP-alpha-D-glucuronate from UDP-alpha-D-glucose: step 1/1.

Developmental stage

Restricted expression to the primary root in young seedlings. Later detected in hypocotyl, leaves and flowers. Ref.7

Induction

Specifically down-regulated by H.schachtii (cyst nematodes) in nematode-induced syncytia. Ref.7 Ref.8

Disruption phenotype

No visible phenotype. Ref.8

Sequence similarities

Belongs to the UDP-glucose/GDP-mannose dehydrogenase family.

Caution

Was originally assigned as UGD1 (Ref.5).

Biophysicochemical properties

Kinetic parameters:

KM=44 µM for NAD+ Ref.7

KM=171 µM for UDP-glucose

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 480480UDP-glucose 6-dehydrogenase 4
PRO_0000312028

Regions

Nucleotide binding8 – 136NAD By similarity
Nucleotide binding86 – 905NAD By similarity
Nucleotide binding127 – 1282NAD By similarity
Nucleotide binding272 – 2754NAD By similarity
Region157 – 1615Substrate binding By similarity
Region216 – 2238Substrate binding By similarity
Region256 – 26914Substrate binding By similarity
Region334 – 3352Substrate binding By similarity

Sites

Active site2721Nucleophile By similarity
Binding site331NAD By similarity
Binding site381NAD By similarity
Binding site1611NAD By similarity
Binding site3421NAD By similarity
Binding site4471Substrate By similarity

Amino acid modifications

Modified residue3501S-nitrosocysteine By similarity

Experimental info

Sequence conflict921Missing in AAP21188. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Q9FM01 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 3FC4FEB2CB647BCB

FASTA48053,097
        10         20         30         40         50         60 
MVKICCIGAG YVGGPTMAVI ALKCPDIEVA VVDISVPRIN AWNSDQLPIY EPGLDDIVKQ 

        70         80         90        100        110        120 
CRGKNLFFST DVEKHVREAD IVFVSVNTPT KTTGLGAGKA ADLTYWESAA RMIADVSVSD 

       130        140        150        160        170        180 
KIVVEKSTVP VKTAEAIEKI LMHNSKGIKF QILSNPEFLA EGTAIADLFN PDRVLIGGRE 

       190        200        210        220        230        240 
TPEGFKAVQT LKEVYANWVP EGQIITTNLW SAELSKLAAN AFLAQRISSV NAMSALCEST 

       250        260        270        280        290        300 
GADVTQVSYA VGTDSRIGSK FLNASVGFGG SCFQKDILNL VYICQCNGLP EVAEYWKQVI 

       310        320        330        340        350        360 
KINDYQKNRF VNRIVSSMFN TVSNKKVAIL GFAFKKDTGD TRETPAIDVC KGLLGDKAQI 

       370        380        390        400        410        420 
SIYDPQVTEE QIQRDLSMKK FDWDHPLHLQ PMSPTTVKQV SVTWDAYEAT KDAHAVCVLT 

       430        440        450        460        470        480 
EWDEFKSLDY QKIFDNMQKP AFIFDGRNIM NVNKLREIGF IVYSIGKPLD PWLKDMPAFV 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB009054, AB010694 Genomic DNA. Translation: BAB11006.1.
CP002688 Genomic DNA. Translation: AED94419.1.
BT006380 mRNA. Translation: AAP21188.1.
RefSeqNP_198748.1. NM_123294.3.
UniGeneAt.20102.
At.71506.

3D structure databases

ProteinModelPortalQ9FM01.
SMRQ9FM01. Positions 3-467.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid19179. 1 interaction.
IntActQ9FM01. 1 interaction.

Proteomic databases

PaxDbQ9FM01.
PRIDEQ9FM01.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G39320.1; AT5G39320.1; AT5G39320.
GeneID833928.
KEGGath:AT5G39320.

Organism-specific databases

TAIRAT5G39320.

Phylogenomic databases

eggNOGCOG1004.
HOGENOMHOG000153773.
InParanoidQ9FM01.
KOK00012.
OMAEMARICD.
PhylomeDBQ9FM01.
ProtClustDBPLN02353.

Enzyme and pathway databases

BioCycARA:AT5G39320-MONOMER.
UniPathwayUPA00038; UER00491.

Gene expression databases

GenevestigatorQ9FM01.

Family and domain databases

Gene3D3.40.50.720. 2 hits.
InterProIPR008927. 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]
PANTHERPTHR11374. PTHR11374. 1 hit.
PTHR11374:SF3. PTHR11374:SF3. 1 hit.
PfamPF00984. UDPG_MGDP_dh. 1 hit.
PF03720. UDPG_MGDP_dh_C. 1 hit.
PF03721. UDPG_MGDP_dh_N. 1 hit.
[Graphical view]
PIRSFPIRSF500133. UDPglc_DH_euk. 1 hit.
PIRSF000124. UDPglc_GDPman_dh. 1 hit.
SMARTSM00984. UDPG_MGDP_dh_C. 1 hit.
[Graphical view]
SUPFAMSSF48179. SSF48179. 1 hit.
SSF52413. SSF52413. 1 hit.
TIGRFAMsTIGR03026. NDP-sugDHase. 1 hit.
ProtoNetSearch...

Entry information

Entry nameUGDH4_ARATH
AccessionPrimary (citable) accession number: Q9FM01
Secondary accession number(s): Q84MD5
Entry history
Integrated into UniProtKB/Swiss-Prot: December 4, 2007
Last sequence update: March 1, 2001
Last modified: March 19, 2014
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names