PDC3_ORYSJ
ID PDC3_ORYSJ Reviewed; 587 AA.
AC Q0D3D2; B7EQF7; P51849; Q84NP9;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Pyruvate decarboxylase 3;
DE Short=PDC;
DE EC=4.1.1.1;
GN Name=PDC3; OrderedLocusNames=Os07g0693100, LOC_Os07g49250;
GN ORFNames=OsJ_024667;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Nipponbare;
RA Nakazono M.;
RT "Oryza sativa pyruvate decarboxylase 3 (PDC3).";
RL Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2-oxocarboxylate + H(+) = an aldehyde + CO2;
CC Xref=Rhea:RHEA:11628, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:17478, ChEBI:CHEBI:35179; EC=4.1.1.1;
CC -!- COFACTOR:
CC Name=a metal cation; Xref=ChEBI:CHEBI:25213;
CC Note=Binds 1 metal ion per subunit.;
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Note=Binds 1 thiamine pyrophosphate per subunit.;
CC -!- SUBUNIT: Homotetramer. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the TPP enzyme family. {ECO:0000305}.
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DR EMBL; AB111050; BAC77042.1; -; mRNA.
DR EMBL; AP004333; BAC75566.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF22641.1; -; Genomic_DNA.
DR EMBL; AP014963; BAT03355.1; -; Genomic_DNA.
DR EMBL; CM000144; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK100433; BAG94604.1; -; mRNA.
DR RefSeq; XP_015646176.1; XM_015790690.1.
DR AlphaFoldDB; Q0D3D2; -.
DR SMR; Q0D3D2; -.
DR STRING; 4530.OS07T0693100-01; -.
DR PaxDb; Q0D3D2; -.
DR PRIDE; Q0D3D2; -.
DR EnsemblPlants; Os07t0693100-01; Os07t0693100-01; Os07g0693100.
DR GeneID; 4344382; -.
DR Gramene; Os07t0693100-01; Os07t0693100-01; Os07g0693100.
DR KEGG; osa:4344382; -.
DR eggNOG; KOG1184; Eukaryota.
DR HOGENOM; CLU_013748_0_2_1; -.
DR InParanoid; Q0D3D2; -.
DR OMA; HYNDIQP; -.
DR OrthoDB; 560466at2759; -.
DR PlantReactome; R-OSA-1119267; Phenylalanine degradation III.
DR PlantReactome; R-OSA-1119460; Isoleucine biosynthesis from threonine.
DR PlantReactome; R-OSA-1119486; IAA biosynthesis I.
DR PlantReactome; R-OSA-1119600; Valine biosynthesis.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000007752; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR ExpressionAtlas; Q0D3D2; baseline and differential.
DR Genevisible; Q0D3D2; OS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0016831; F:carboxy-lyase activity; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0004737; F:pyruvate decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:InterPro.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012000; Thiamin_PyroP_enz_cen_dom.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR012110; TPP_enzyme.
DR InterPro; IPR011766; TPP_enzyme-bd_C.
DR PANTHER; PTHR43452; PTHR43452; 1.
DR Pfam; PF02775; TPP_enzyme_C; 1.
DR Pfam; PF00205; TPP_enzyme_M; 1.
DR Pfam; PF02776; TPP_enzyme_N; 1.
DR PIRSF; PIRSF036565; Pyruvt_ip_decrb; 1.
DR SUPFAM; SSF52467; SSF52467; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
PE 2: Evidence at transcript level;
KW Decarboxylase; Lyase; Magnesium; Metal-binding; Reference proteome;
KW Thiamine pyrophosphate.
FT CHAIN 1..587
FT /note="Pyruvate decarboxylase 3"
FT /id="PRO_0000090781"
FT REGION 415..496
FT /note="Thiamine pyrophosphate binding"
FT BINDING 48
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 135
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 464
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 491
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 493
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 497
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 587 AA; 62642 MW; C5F979FE251A7250 CRC64;
MESNGGGGGS PKEAAVVVPS SGDATLGGHL ARRLVQVGVS DVFAVPGDFN LTLLDHLIAE
PGLRVVGCCN ELNAGYAADG YARARGVGAC AVTFTVGGLS VLNAIGGAYS ENLPLICIVG
GPNSNDYGTN RILHHTIGLP DFSQELRCFQ PLTCYQAVVN NLDDAHDQID RAISTAIRES
KPVYISVSCN LPAVPHPTFS RDPVPYFLSP RLSNQASLHA ALDATLAFLD KAVKPVLVAG
PKLRVAKAGG AFVDLADASG HAVAAMPSAK GLVPETLPRF IGTYWGAVST AFCAEIVESA
DAYLFAGPIF NDYSSVGYSC LLKKEKAVVV QPDRVTVGNG PAFGCVMMRD FLSELAKRVR
KNTTAFDNYK RIFVPEGQLP ECEAGEALRV NVLFKHIQRM IGGTEIGAVM AETGDSWFNC
QKLRLPEGCG YEFQMQYGSI GWSVGALLGY AQAVQKRVVA CIGDGSFQVT AQDVSTMLRC
GQRSIIFLIN NGGYTIEVEI HDGPYNVIKN WDYVGLVNAI HNGEGRCWAT RVRCEEELEA
AIATATGDKA DSLCFIEVVA HKDDTSKELL EWGSRVSAAN SRPPNPQ
