PDC1_ORYSJ
ID PDC1_ORYSJ Reviewed; 605 AA.
AC Q0DHF6; P51847; Q6AUJ9;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Pyruvate decarboxylase 1;
DE Short=PDC;
DE EC=4.1.1.1;
GN Name=PDC1; OrderedLocusNames=Os05g0469600, LOC_Os05g39310;
GN ORFNames=OsJ_018109, OSJNBa0052E20.2;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(2005).
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; AC121364; AAT93945.1; -; Genomic_DNA.
DR EMBL; AP008211; BAF17717.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS94476.1; -; Genomic_DNA.
DR EMBL; CM000142; EAZ34626.1; -; Genomic_DNA.
DR EMBL; AK100678; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015637741.1; XM_015782255.1.
DR AlphaFoldDB; Q0DHF6; -.
DR SMR; Q0DHF6; -.
DR STRING; 4530.OS05T0469600-01; -.
DR PaxDb; Q0DHF6; -.
DR PRIDE; Q0DHF6; -.
DR EnsemblPlants; Os05t0469600-01; Os05t0469600-01; Os05g0469600.
DR GeneID; 4339066; -.
DR Gramene; Os05t0469600-01; Os05t0469600-01; Os05g0469600.
DR KEGG; osa:4339066; -.
DR eggNOG; KOG1184; Eukaryota.
DR HOGENOM; CLU_013748_0_2_1; -.
DR InParanoid; Q0DHF6; -.
DR OMA; YPNVRMK; -.
DR OrthoDB; 560466at2759; -.
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 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR ExpressionAtlas; Q0DHF6; differential.
DR Genevisible; Q0DHF6; 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..605
FT /note="Pyruvate decarboxylase 1"
FT /id="PRO_0000090779"
FT REGION 432..514
FT /note="Thiamine pyrophosphate binding"
FT BINDING 67
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 154
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 482
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 509
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 511
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 515
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 605 AA; 65155 MW; 78406A557955301B CRC64;
MELALVGNPS NGVAKPSCNS VGSLPVVSSN AVINPPVTSA AGATLGRHLA RRLVQIGATD
VFAVPGDFNL TLLDYLIAEP GLKLIGCCNE LNAGYAADGY ARARGVGACA VTFTVGGLSV
LNAIAGAYSE NLPVICIVGG PNSNDYGTNR ILHHTIGLPD FSQELRCFQT ITCYQAVINN
LDDAHEQIDT AIATALRESK PVYISVGCNL AGLSHPTFSR EPVPLFISPR LSNKANLEYA
VEAAADFLNK AVKPVMVGGP KIRVAKAKKA FAGIAESSGY PFAVMPSAKG LVPEHHPRFI
GTYWGAVSTT FCAEIVESAD AYLFAGPIFN DYSSVGYSLL LKREKAVIVQ PDRVVVGNGP
AFGCILMTEF LDALAKRLDR NTTAYDNYRR IFIPDREPPN GQPDEPLRVN ILFKHIKEML
SGDTAVIAET GDSWFNCQKL RLPEGCGYEF QMQYGSIGWS VGATLGYAQA AKDKRVISCI
GDGSFQMTAQ DVSTMLRCGQ KSIIFLINNG GYTIEVEIHD GPYNVIKNWD YTGLIDAIHN
SDGNCWTKKV RTEEELIEAI ATATGAKKDC LCFIEIIVHK DDTSKELLEW GSRVSAANSR
PPNPQ
