UGDH4_ARATH
ID UGDH4_ARATH Reviewed; 480 AA.
AC Q9FM01; Q84MD5;
DT 04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=UDP-glucose 6-dehydrogenase 4 {ECO:0000303|PubMed:18057039};
DE Short=At-UGD4 {ECO:0000303|PubMed:18057039};
DE Short=UDP-Glc dehydrogenase 4 {ECO:0000303|PubMed:18057039};
DE Short=UDP-GlcDH 4 {ECO:0000303|PubMed:18057039};
DE Short=UDPGDH 4 {ECO:0000303|PubMed:18057039};
DE EC=1.1.1.22 {ECO:0000269|PubMed:18057039};
GN Name=UGD4 {ECO:0000303|PubMed:18057039, ECO:0000303|PubMed:22848518};
GN Synonyms=UGD1 {ECO:0000303|PubMed:15134748};
GN OrderedLocusNames=At5g39320 {ECO:0000312|Araport:AT5G39320};
GN ORFNames=K3K3.170 {ECO:0000312|EMBL:BAB11006.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9628582; DOI=10.1093/dnares/5.1.41;
RA Sato S., Kaneko T., Kotani H., Nakamura Y., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence
RT features of the regions of 1,456,315 bp covered by nineteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:41-54(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9679202; DOI=10.1093/dnares/5.2.131;
RA Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
RT features of the regions of 1,381,565 bp covered by twenty one physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:131-145(1998).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP GENE FAMILY.
RX PubMed=11554483; DOI=10.1023/a:1010671129803;
RA Reiter W.-D., Vanzin G.F.;
RT "Molecular genetics of nucleotide sugar interconversion pathways in
RT plants.";
RL Plant Mol. Biol. 47:95-113(2001).
RN [6]
RP REVIEW.
RX PubMed=15134748; DOI=10.1016/j.pbi.2004.03.004;
RA Seifert G.J.;
RT "Nucleotide sugar interconversions and cell wall biosynthesis: how to bring
RT the inside to the outside.";
RL Curr. Opin. Plant Biol. 7:277-284(2004).
RN [7]
RP FUNCTION, GENE FAMILY, NOMENCLATURE, DEVELOPMENTAL STAGE,
RP BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, PATHWAY, AND ACTIVITY
RP REGULATION.
RC STRAIN=cv. Columbia;
RX PubMed=18057039; DOI=10.1093/jxb/erm209;
RA Klinghammer M., Tenhaken R.;
RT "Genome-wide analysis of the UDP-glucose dehydrogenase gene family in
RT Arabidopsis, a key enzyme for matrix polysaccharides in cell walls.";
RL J. Exp. Bot. 58:3609-3621(2007).
RN [8]
RP DISRUPTION PHENOTYPE, INDUCTION, AND PATHWAY.
RC STRAIN=cv. Columbia;
RX PubMed=22848518; DOI=10.1371/journal.pone.0041515;
RA Siddique S., Sobczak M., Tenhaken R., Grundler F.M., Bohlmann H.;
RT "Cell wall ingrowths in nematode induced syncytia require UGD2 and UGD3.";
RL PLoS ONE 7:E41515-E41515(2012).
CC -!- FUNCTION: Involved in the biosynthesis of UDP-glucuronic acid (UDP-
CC GlcA), providing nucleotide sugars for cell-wall polymers.
CC {ECO:0000269|PubMed:18057039}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + 2 NAD(+) + UDP-alpha-D-glucose = 3 H(+) + 2 NADH + UDP-
CC alpha-D-glucuronate; Xref=Rhea:RHEA:23596, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58052, ChEBI:CHEBI:58885; EC=1.1.1.22;
CC Evidence={ECO:0000269|PubMed:18057039};
CC -!- ACTIVITY REGULATION: Inhibited by UDP-xylose.
CC {ECO:0000269|PubMed:18057039}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=44 uM for NAD(+) {ECO:0000269|PubMed:18057039};
CC KM=171 uM for UDP-glucose {ECO:0000269|PubMed:18057039};
CC -!- PATHWAY: Nucleotide-sugar biosynthesis; UDP-alpha-D-glucuronate
CC biosynthesis; UDP-alpha-D-glucuronate from UDP-alpha-D-glucose: step
CC 1/1. {ECO:0000269|PubMed:18057039, ECO:0000269|PubMed:22848518}.
CC -!- DEVELOPMENTAL STAGE: Restricted expression to the primary root in young
CC seedlings. Later detected in hypocotyl, leaves and flowers.
CC {ECO:0000269|PubMed:18057039}.
CC -!- INDUCTION: Specifically down-regulated by H.schachtii (cyst nematodes)
CC in nematode-induced syncytia. {ECO:0000269|PubMed:22848518}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:22848518}.
CC -!- SIMILARITY: Belongs to the UDP-glucose/GDP-mannose dehydrogenase
CC family. {ECO:0000305}.
CC -!- CAUTION: Was originally assigned as UGD1.
CC {ECO:0000305|PubMed:11554483}.
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DR EMBL; AB009054; BAB11006.1; -; Genomic_DNA.
DR EMBL; AB010694; BAB11006.1; JOINED; Genomic_DNA.
DR EMBL; CP002688; AED94419.1; -; Genomic_DNA.
DR EMBL; BT006380; AAP21188.1; -; mRNA.
DR RefSeq; NP_198748.1; NM_123294.4.
DR AlphaFoldDB; Q9FM01; -.
DR SMR; Q9FM01; -.
DR BioGRID; 19179; 1.
DR IntAct; Q9FM01; 1.
DR STRING; 3702.AT5G39320.1; -.
DR iPTMnet; Q9FM01; -.
DR PaxDb; Q9FM01; -.
DR PRIDE; Q9FM01; -.
DR ProteomicsDB; 245257; -.
DR EnsemblPlants; AT5G39320.1; AT5G39320.1; AT5G39320.
DR GeneID; 833928; -.
DR Gramene; AT5G39320.1; AT5G39320.1; AT5G39320.
DR KEGG; ath:AT5G39320; -.
DR Araport; AT5G39320; -.
DR TAIR; locus:2157275; AT5G39320.
DR eggNOG; KOG2666; Eukaryota.
DR HOGENOM; CLU_023810_7_0_1; -.
DR InParanoid; Q9FM01; -.
DR OMA; EYLYPGC; -.
DR OrthoDB; 915490at2759; -.
DR PhylomeDB; Q9FM01; -.
DR BioCyc; ARA:AT5G39320-MON; -.
DR BRENDA; 1.1.1.22; 399.
DR SABIO-RK; Q9FM01; -.
DR UniPathway; UPA00038; UER00491.
DR PRO; PR:Q9FM01; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FM01; baseline and differential.
DR Genevisible; Q9FM01; AT.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0003979; F:UDP-glucose 6-dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0006024; P:glycosaminoglycan biosynthetic process; IBA:GO_Central.
DR GO; GO:0006065; P:UDP-glucuronate biosynthetic process; IDA:UniProtKB.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR017476; UDP-Glc/GDP-Man.
DR InterPro; IPR014027; UDP-Glc/GDP-Man_DH_C.
DR InterPro; IPR036220; UDP-Glc/GDP-Man_DH_C_sf.
DR InterPro; IPR014026; UDP-Glc/GDP-Man_DH_dimer.
DR InterPro; IPR001732; UDP-Glc/GDP-Man_DH_N.
DR InterPro; IPR028356; UDPglc_DH_euk.
DR PANTHER; PTHR11374; PTHR11374; 1.
DR Pfam; PF00984; UDPG_MGDP_dh; 1.
DR Pfam; PF03720; UDPG_MGDP_dh_C; 1.
DR Pfam; PF03721; UDPG_MGDP_dh_N; 1.
DR PIRSF; PIRSF500133; UDPglc_DH_euk; 1.
DR PIRSF; PIRSF000124; UDPglc_GDPman_dh; 1.
DR SMART; SM00984; UDPG_MGDP_dh_C; 1.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR SUPFAM; SSF52413; SSF52413; 1.
DR TIGRFAMs; TIGR03026; NDP-sugDHase; 1.
PE 1: Evidence at protein level;
KW NAD; Oxidoreductase; Reference proteome.
FT CHAIN 1..480
FT /note="UDP-glucose 6-dehydrogenase 4"
FT /id="PRO_0000312028"
FT ACT_SITE 272
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 3..20
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 33
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 38
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 90
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 128
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 157..161
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 161
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 216..223
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 216
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 256..269
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 269
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 275
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 334
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 335
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 342
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT BINDING 447
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P0C0F4"
FT CONFLICT 92
FT /note="Missing (in Ref. 4; AAP21188)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 480 AA; 53097 MW; 3FC4FEB2CB647BCB CRC64;
MVKICCIGAG YVGGPTMAVI ALKCPDIEVA VVDISVPRIN AWNSDQLPIY EPGLDDIVKQ
CRGKNLFFST DVEKHVREAD IVFVSVNTPT KTTGLGAGKA ADLTYWESAA RMIADVSVSD
KIVVEKSTVP VKTAEAIEKI LMHNSKGIKF QILSNPEFLA EGTAIADLFN PDRVLIGGRE
TPEGFKAVQT LKEVYANWVP EGQIITTNLW SAELSKLAAN AFLAQRISSV NAMSALCEST
GADVTQVSYA VGTDSRIGSK FLNASVGFGG SCFQKDILNL VYICQCNGLP EVAEYWKQVI
KINDYQKNRF VNRIVSSMFN TVSNKKVAIL GFAFKKDTGD TRETPAIDVC KGLLGDKAQI
SIYDPQVTEE QIQRDLSMKK FDWDHPLHLQ PMSPTTVKQV SVTWDAYEAT KDAHAVCVLT
EWDEFKSLDY QKIFDNMQKP AFIFDGRNIM NVNKLREIGF IVYSIGKPLD PWLKDMPAFV
