DPYD_ARATH
ID DPYD_ARATH Reviewed; 426 AA.
AC Q9LVI9;
DT 01-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Dihydropyrimidine dehydrogenase (NADP(+)), chloroplastic {ECO:0000303|PubMed:19413687};
DE Short=DHPDH {ECO:0000303|PubMed:19413687};
DE Short=DPD;
DE EC=1.3.1.2 {ECO:0000269|PubMed:19413687};
DE AltName: Full=Dihydroorotate dehydrogenase-like protein {ECO:0000303|PubMed:12369616};
DE AltName: Full=Dihydrothymine dehydrogenase;
DE AltName: Full=Dihydrouracil dehydrogenase;
DE AltName: Full=Protein PYRIMIDINE 1 {ECO:0000303|PubMed:19413687};
DE Flags: Precursor;
GN Name=PYD1 {ECO:0000303|PubMed:19413687};
GN Synonyms=PYD1A {ECO:0000303|Ref.1};
GN OrderedLocusNames=At3g17810 {ECO:0000312|Araport:AT3G17810};
GN ORFNames=MEB5.3 {ECO:0000312|EMBL:BAB02704.1};
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 {ECO:0000312|Proteomes:UP000006548};
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Gojkovic Z., Sandrini M.P.B., Piskur J.;
RT "Dihydropyrimidine dehydrogenases and the evolution of the pyrimidine
RT degradation pathway.";
RL Submitted (SEP-2002) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
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 IDENTIFICATION.
RX PubMed=12369616; DOI=10.1023/a:1019854531254;
RA Giermann N., Schroder M., Ritter T., Zrenner R.;
RT "Molecular analysis of de novo pyrimidine synthesis in solanaceous
RT species.";
RL Plant Mol. Biol. 50:393-403(2002).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, DEVELOPMENTAL STAGE, INDUCTION BY NITROGEN
RP LIMITATION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=19413687; DOI=10.1111/j.1469-8137.2009.02843.x;
RA Zrenner R., Riegler H., Marquard C.R., Lange P.R., Geserick C.,
RA Bartosz C.E., Chen C.T., Slocum R.D.;
RT "A functional analysis of the pyrimidine catabolic pathway in
RT Arabidopsis.";
RL New Phytol. 183:117-132(2009).
RN [7]
RP FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION,
RP AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia;
RX PubMed=21865177; DOI=10.1093/jxb/err251;
RA Cornelius S., Witz S., Rolletschek H., Mohlmann T.;
RT "Pyrimidine degradation influences germination seedling growth and
RT production of Arabidopsis seeds.";
RL J. Exp. Bot. 62:5623-5632(2011).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-45, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER SER-44, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Involved in pyrimidine base degradation. Catalyzes the
CC reduction of uracil to 5,6-dihydrouracil (DHU) by using NADH as a
CC specific cosubstrate and the reduction of thymine to 5,6-dihydrothymine
CC (DHT). Involved in the recycling of nitrogen from nucleobases to
CC general nitrogen metabolism. {ECO:0000269|PubMed:19413687,
CC ECO:0000269|PubMed:21865177}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouracil + NADP(+) = H(+) + NADPH + uracil;
CC Xref=Rhea:RHEA:18093, ChEBI:CHEBI:15378, ChEBI:CHEBI:15901,
CC ChEBI:CHEBI:17568, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.3.1.2;
CC Evidence={ECO:0000305};
CC -!- PATHWAY: Amino-acid biosynthesis; beta-alanine biosynthesis.
CC {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:19413687, ECO:0000269|PubMed:21865177}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems, siliques and
CC flowers. Highly expressed ion dry seeds. {ECO:0000269|PubMed:21865177}.
CC -!- DEVELOPMENTAL STAGE: Up-regulated at days 4 and 5 after germination and
CC during senescence. {ECO:0000269|PubMed:19413687,
CC ECO:0000269|PubMed:21865177}.
CC -!- INDUCTION: Up-regulated by nitrogen limitation.
CC {ECO:0000269|PubMed:19413687}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype, but impaired degradation of
CC both thymine and uracil (PubMed:19413687, PubMed:21865177). Slower
CC germination and 2 days delay in seedling development (PubMed:21865177).
CC {ECO:0000269|PubMed:19413687, ECO:0000269|PubMed:21865177}.
CC -!- SIMILARITY: Belongs to the dihydropyrimidine dehydrogenase family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF545062; AAN64919.1; -; mRNA.
DR EMBL; AB019230; BAB02704.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76010.1; -; Genomic_DNA.
DR EMBL; AY035029; AAK59534.1; -; mRNA.
DR EMBL; AY059103; AAL15209.1; -; mRNA.
DR RefSeq; NP_188408.1; NM_112662.4.
DR AlphaFoldDB; Q9LVI9; -.
DR SMR; Q9LVI9; -.
DR STRING; 3702.AT3G17810.1; -.
DR iPTMnet; Q9LVI9; -.
DR PaxDb; Q9LVI9; -.
DR PRIDE; Q9LVI9; -.
DR ProteomicsDB; 241252; -.
DR EnsemblPlants; AT3G17810.1; AT3G17810.1; AT3G17810.
DR GeneID; 821049; -.
DR Gramene; AT3G17810.1; AT3G17810.1; AT3G17810.
DR KEGG; ath:AT3G17810; -.
DR Araport; AT3G17810; -.
DR TAIR; locus:2088570; AT3G17810.
DR eggNOG; KOG1799; Eukaryota.
DR HOGENOM; CLU_042042_1_1_1; -.
DR InParanoid; Q9LVI9; -.
DR OMA; MVPCVEE; -.
DR OrthoDB; 1194348at2759; -.
DR PhylomeDB; Q9LVI9; -.
DR BioCyc; ARA:AT3G17810-MON; -.
DR BioCyc; MetaCyc:AT3G17810-MON; -.
DR UniPathway; UPA00131; -.
DR PRO; PR:Q9LVI9; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LVI9; baseline and differential.
DR Genevisible; Q9LVI9; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0017113; F:dihydropyrimidine dehydrogenase (NADP+) activity; IMP:TAIR.
DR GO; GO:0051536; F:iron-sulfur cluster binding; IBA:GO_Central.
DR GO; GO:0050661; F:NADP binding; IBA:GO_Central.
DR GO; GO:0002058; F:uracil binding; IBA:GO_Central.
DR GO; GO:0019483; P:beta-alanine biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0043562; P:cellular response to nitrogen levels; IEP:TAIR.
DR GO; GO:0006210; P:thymine catabolic process; IBA:GO_Central.
DR GO; GO:0006212; P:uracil catabolic process; IMP:TAIR.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR005720; Dihydroorotate_DH.
DR InterPro; IPR044512; DPYD.
DR PANTHER; PTHR43073; PTHR43073; 1.
DR Pfam; PF01180; DHO_dh; 1.
DR TIGRFAMs; TIGR01037; pyrD_sub1_fam; 1.
PE 1: Evidence at protein level;
KW Acetylation; Chloroplast; NADP; Oxidoreductase; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..44
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 45..426
FT /note="Dihydropyrimidine dehydrogenase (NADP(+)),
FT chloroplastic"
FT /evidence="ECO:0000255"
FT /id="PRO_0000432454"
FT REGION 395..414
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 191
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PIRSR:PIRSR000164-1"
FT BINDING 129
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q28943"
FT BINDING 188..190
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q28943"
FT BINDING 256..257
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q28943"
FT MOD_RES 45
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 426 AA; 46847 MW; 0DA1BAEE08F90A18 CRC64;
MASMSFALNR FSGLSSKTTL SADFDPSSRR SFLPPTRVGL KISSAAESEP DLSVTVNGLK
MPNPFVIGSG PPGTNYTVMK RAFDEGWGAV IAKTVSLDAS KVINVTPRYA RLRTGSNGSA
KTDVIGWQNI ELISDRPLET MLKEFERLKK EYPDRILIAS VMEEYNKTAW EELIDRVEQT
GVDALEINFS CPHGMPERRM GAAVGQDCAL LDEVCGWINA KATVPVWAKM TPNITDITEP
ARVSLKSGCE GIAAINTIMS VMGIDMKTLR PEPCVEGYST PGGYSYKAVR PIALAKVMNI
AKMMKSEFSE DRSLSGIGGV ETGYDAAEFI LLGSNTVQVC TGVMMHGYGH VKTLCAELKD
FMKQHNFSTI EEFRGHSLQY FTTHTDLVKR QKEAVEQRKA EKRGLKSDKD WTGDGFVKET
ESMVSN
