ID PDC2_ORYSJ Reviewed; 605 AA.
AC Q10MW3; P51848;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 27-MAR-2024, entry version 104.
DE RecName: Full=Pyruvate decarboxylase 2;
DE Short=PDC;
DE EC=4.1.1.1;
GN Name=PDC2; OrderedLocusNames=Os03g0293500, LOC_Os03g18220;
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=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(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 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; DP000009; ABF95411.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF11725.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS83688.1; -; Genomic_DNA.
DR EMBL; AK101594; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015631876.1; XM_015776390.1.
DR AlphaFoldDB; Q10MW3; -.
DR SMR; Q10MW3; -.
DR STRING; 39947.Q10MW3; -.
DR PaxDb; 39947-Q10MW3; -.
DR EnsemblPlants; Os03t0293500-02; Os03t0293500-02; Os03g0293500.
DR GeneID; 4332519; -.
DR Gramene; Os03t0293500-02; Os03t0293500-02; Os03g0293500.
DR KEGG; osa:4332519; -.
DR eggNOG; KOG1184; Eukaryota.
DR HOGENOM; CLU_013748_0_2_1; -.
DR InParanoid; Q10MW3; -.
DR OMA; YIFLPLD; -.
DR OrthoDB; 1000728at2759; -.
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 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q10MW3; baseline and differential.
DR Genevisible; Q10MW3; OS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0004737; F:pyruvate decarboxylase activity; IBA:GO_Central.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:InterPro.
DR GO; GO:0000949; P:aromatic amino acid family catabolic process to alcohol via Ehrlich pathway; IBA:GO_Central.
DR CDD; cd02005; TPP_PDC_IPDC; 1.
DR CDD; cd07038; TPP_PYR_PDC_IPDC_like; 1.
DR Gene3D; 3.40.50.970; -; 2.
DR Gene3D; 3.40.50.1220; TPP-binding domain; 1.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR012110; PDC/IPDC-like.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012000; Thiamin_PyroP_enz_cen_dom.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR011766; TPP_enzyme_TPP-bd.
DR InterPro; IPR047214; TPP_PDC_IPDC.
DR InterPro; IPR047213; TPP_PYR_PDC_IPDC-like.
DR PANTHER; PTHR43452; PYRUVATE DECARBOXYLASE; 1.
DR PANTHER; PTHR43452:SF39; PYRUVATE DECARBOXYLASE 2; 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; DHS-like NAD/FAD-binding domain; 1.
DR SUPFAM; SSF52518; Thiamin diphosphate-binding fold (THDP-binding); 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 2"
FT /id="PRO_0000090780"
FT REGION 433..515
FT /note="Thiamine pyrophosphate binding"
FT BINDING 68
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 155
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 483
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 510
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 512
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 516
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 605 AA; 64719 MW; 3D664983C10D88A9 CRC64;
METHIGSVDG AAAAADNGAV GCPASAVGCP MTSARPAPVS AGEASLGRHL ARRLVQVGVS
DVFAVPGDFN LTLLDHLIAE PGLRLVGCCN ELNAGYAADG YARARGVGAC AVTFTVGGLS
VLNAIAGAYS ENLPVICIAG GPNSNDYGTN RILHHTIGLP DFSQELRCFQ TVTCHQAVVT
NLEDAHEQID TAIATALRES KPVYLSISCN LPGLPHPTFS RDPVPFFLAP RLSNKMGLEA
AVEATVEFLN KAVKPVLVGG PKLRVAKAGK AFVDLVDASG YAYAVMPSAK GLVPETHPHF
IGTYWGAVST AFCAEIVESA DAYLFAGPIF NDYSSVGYSF LLKKDKAIIV QPERVIVGNG
PAFGCVMMKE FLSELAKRVN KNTTAYENYK RIFVPEGQPL ESEPNEPLRV NVLFKHVQKM
LNSDSAVIAE TGDSWFNCQK LKLPEGCGYE FQMQYGSIGW SVGALLGYAQ GAKDKRVIAC
IGDGSFQVTA QDVSTMIRCA QNSIIFLINN GGYTIEVEIH DGPYNVIKNW NYTGLVDAIH
NGEGKCWTSK VKCEEELTEA IGMALGEKDC LCFIEVIAHK DDTSKELLEW GSRVSAANSR
PPNPQ
//
