DPYS_ARATH
ID DPYS_ARATH Reviewed; 531 AA.
AC Q9FMP3;
DT 01-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Dihydropyrimidinase {ECO:0000303|PubMed:12626710};
DE EC=3.5.2.2 {ECO:0000269|PubMed:19413687};
DE AltName: Full=Dihydropyrimidine amidohydrolase {ECO:0000303|PubMed:12626710};
DE AltName: Full=Protein PYRIMIDINE 2 {ECO:0000303|PubMed:12626710};
GN Name=PYD2 {ECO:0000303|PubMed:12626710};
GN OrderedLocusNames=At5g12200 {ECO:0000312|Araport:AT5G12200};
GN ORFNames=MXC9.16 {ECO:0000312|EMBL:BAB10038.1};
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], AND FUNCTION.
RX PubMed=12626710; DOI=10.1093/nar/gkg258;
RA Gojkovic Z., Rislund L., Andersen B., Sandrini M.P., Cook P.F.,
RA Schnackerz K.D., Piskur J.;
RT "Dihydropyrimidine amidohydrolases and dihydroorotases share the same
RT origin and several enzymatic properties.";
RL Nucleic Acids Res. 31:1683-1692(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
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 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).
CC -!- FUNCTION: Catalyzes the second step of the reductive pyrimidine
CC degradation, the reversible hydrolytic ring opening of
CC dihydropyrimidines. Can catalyze the ring opening of 5,6-dihydrouracil
CC to N-carbamoyl-alanine and of 5,6-dihydrothymine to N-carbamoyl-amino
CC isobutyrate. Involved in the recycling of nitrogen from nucleobases to
CC general nitrogen metabolism. {ECO:0000269|PubMed:12626710,
CC ECO:0000269|PubMed:19413687}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,6-dihydrouracil + H2O = 3-(carbamoylamino)propanoate + H(+);
CC Xref=Rhea:RHEA:16121, ChEBI:CHEBI:11892, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15901; EC=3.5.2.2;
CC Evidence={ECO:0000269|PubMed:19413687};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q9P903};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000250|UniProtKB:Q9P903};
CC -!- PATHWAY: Amino-acid biosynthesis; beta-alanine biosynthesis.
CC {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250|UniProtKB:Q55DL0}.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum
CC {ECO:0000269|PubMed:19413687}.
CC -!- DEVELOPMENTAL STAGE: Up-regulated between days 3 and 12 after
CC germination and during senescence. {ECO:0000269|PubMed:19413687}.
CC -!- INDUCTION: Up-regulated by nitrogen limitation.
CC {ECO:0000269|PubMed:19413687}.
CC -!- PTM: Carboxylation allows a single lysine to coordinate two zinc ions.
CC {ECO:0000250|UniProtKB:Q9P903}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype, but unable to grow on
CC uracil as sole nitrogen source. {ECO:0000269|PubMed:19413687}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Hydantoinase/dihydropyrimidinase family. {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; AF465755; AAO33381.1; -; mRNA.
DR EMBL; AB007727; BAB10038.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91773.1; -; Genomic_DNA.
DR RefSeq; NP_568258.2; NM_121258.4.
DR AlphaFoldDB; Q9FMP3; -.
DR SMR; Q9FMP3; -.
DR IntAct; Q9FMP3; 1.
DR STRING; 3702.AT5G12200.1; -.
DR MEROPS; M38.973; -.
DR iPTMnet; Q9FMP3; -.
DR PaxDb; Q9FMP3; -.
DR PRIDE; Q9FMP3; -.
DR ProteomicsDB; 241253; -.
DR EnsemblPlants; AT5G12200.1; AT5G12200.1; AT5G12200.
DR GeneID; 831093; -.
DR Gramene; AT5G12200.1; AT5G12200.1; AT5G12200.
DR KEGG; ath:AT5G12200; -.
DR Araport; AT5G12200; -.
DR TAIR; locus:2177048; AT5G12200.
DR eggNOG; KOG2584; Eukaryota.
DR HOGENOM; CLU_015572_2_1_1; -.
DR InParanoid; Q9FMP3; -.
DR OMA; SAETHHM; -.
DR OrthoDB; 719800at2759; -.
DR PhylomeDB; Q9FMP3; -.
DR BioCyc; MetaCyc:AT5G12200-MON; -.
DR BRENDA; 3.5.2.2; 399.
DR UniPathway; UPA00131; -.
DR PRO; PR:Q9FMP3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FMP3; baseline and differential.
DR Genevisible; Q9FMP3; AT.
DR GO; GO:0012505; C:endomembrane system; IDA:TAIR.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA:TAIR.
DR GO; GO:0005794; C:Golgi apparatus; HDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0004157; F:dihydropyrimidinase activity; IGI:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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:0006208; P:pyrimidine nucleobase catabolic process; IBA:GO_Central.
DR GO; GO:0006212; P:uracil catabolic process; IMP:TAIR.
DR CDD; cd01314; D-HYD; 1.
DR Gene3D; 2.30.40.10; -; 1.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR011778; Hydantoinase/dihydroPyrase.
DR InterPro; IPR011059; Metal-dep_hydrolase_composite.
DR InterPro; IPR032466; Metal_Hydrolase.
DR Pfam; PF01979; Amidohydro_1; 1.
DR SUPFAM; SSF51338; SSF51338; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR02033; D-hydantoinase; 1.
PE 1: Evidence at protein level;
KW Endoplasmic reticulum; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..531
FT /note="Dihydropyrimidinase"
FT /id="PRO_0000432455"
FT BINDING 103
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 105
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 193
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /note="via carbamate group"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 193
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /note="via carbamate group"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 198
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 226
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 282
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 332
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 359
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT BINDING 380
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
FT MOD_RES 193
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000250|UniProtKB:Q9P903"
SQ SEQUENCE 531 AA; 57991 MW; F6DE523D73027789 CRC64;
MALDAFFFIV SLFLLFPSPS ASESTTQFCS AGRENGVGSC GVSSTRILIK GGTVVNAHHQ
ELADVYVENG IIVAVQPNIK VGDEVTVLDA TGKFVMPGGI DPHTHLAMEF MGTETIDDFF
SGQAAALAGG TTMHIDFVIP VNGNLVAGFE AYENKSRESC MDYGFHMAIT KWDEGVSRDM
EMLVKEKGIN SFKFFLAYKG SLMVTDDLLL EGLKRCKSLG ALAMVHAENG DAVFEGQKRM
IELGITGPEG HALSRPPVLE GEATARAIRL ARFINTPLYV VHVMSVDAMD EIAKARKSGQ
KVIGEPVVSG LILDDHWLWD PDFTIASKYV MSPPIRPVGH GKALQDALST GILQLVGTDH
CTFNSTQKAL GLDDFRRIPN GVNGLEERMH LIWDTMVESG QLSATDYVRI TSTECARIFN
IYPRKGAILA GSDADIIILN PNSSYEISSK SHHSRSDTNV YEGRRGKGKV EVTIAGGRIV
WENEELKVVP RSGKYIEMPP FSYLFDGIEK SDANYLSSLR APVKRVRTEA T
