ID   DCDA_ORYSJ              Reviewed;         490 AA.
AC   Q6ZG77; A3A6C9; A3A6D0; B7ED21;
DT   23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 108.
DE   RecName: Full=Probable diaminopimelate decarboxylase, chloroplastic;
DE            Short=DAP decarboxylase;
DE            Short=DAPDC;
DE            EC=4.1.1.20;
DE   Flags: Precursor;
GN   Name=LYSA; OrderedLocusNames=Os02g0440000, LOC_Os02g24354;
GN   ORFNames=OJ1008_E02.6, OsJ_006351/OsJ_006352;
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=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   [2]
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   [3]
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   [4]
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   [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   -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC       diaminopimelate (meso-DAP) to L-lysine. {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H(+) + meso-2,6-diaminoheptanedioate = CO2 + L-lysine;
CC         Xref=Rhea:RHEA:15101, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:32551, ChEBI:CHEBI:57791; EC=4.1.1.20;
CC   -!- COFACTOR:
CC       Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC         Evidence={ECO:0000250};
CC   -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC       pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC   -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC       LysA subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=EAZ22869.1; Type=Erroneous gene model prediction; Evidence={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; AP004151; BAD16980.1; -; Genomic_DNA.
DR   EMBL; AP008208; BAF08658.1; -; Genomic_DNA.
DR   EMBL; AP014958; BAS78484.1; -; Genomic_DNA.
DR   EMBL; CM000139; EAZ22869.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AK067100; BAG90268.1; -; mRNA.
DR   RefSeq; XP_015627100.1; XM_015771614.1.
DR   AlphaFoldDB; Q6ZG77; -.
DR   SMR; Q6ZG77; -.
DR   STRING; 4530.OS02T0440000-01; -.
DR   PaxDb; Q6ZG77; -.
DR   PRIDE; Q6ZG77; -.
DR   EnsemblPlants; Os02t0440000-01; Os02t0440000-01; Os02g0440000.
DR   GeneID; 4329234; -.
DR   Gramene; Os02t0440000-01; Os02t0440000-01; Os02g0440000.
DR   KEGG; osa:4329234; -.
DR   eggNOG; KOG0622; Eukaryota.
DR   InParanoid; Q6ZG77; -.
DR   OMA; YCRSMAS; -.
DR   OrthoDB; 725914at2759; -.
DR   BRENDA; 4.1.1.20; 4460.
DR   PlantReactome; R-OSA-1119273; Lysine biosynthesis I.
DR   PlantReactome; R-OSA-1119283; Lysine biosynthesis II.
DR   PlantReactome; R-OSA-1119419; Lysine biosynthesis VI.
DR   UniPathway; UPA00034; UER00027.
DR   Proteomes; UP000000763; Chromosome 2.
DR   Proteomes; UP000007752; Chromosome 2.
DR   Proteomes; UP000059680; Chromosome 2.
DR   ExpressionAtlas; Q6ZG77; baseline and differential.
DR   Genevisible; Q6ZG77; OS.
DR   GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR   GO; GO:0008836; F:diaminopimelate decarboxylase activity; IBA:GO_Central.
DR   GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
DR   CDD; cd06828; PLPDE_III_DapDC; 1.
DR   Gene3D; 2.40.37.10; -; 1.
DR   Gene3D; 3.20.20.10; -; 1.
DR   HAMAP; MF_02120; LysA; 1.
DR   InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR   InterPro; IPR002986; DAP_deCOOHase_LysA.
DR   InterPro; IPR022643; De-COase2_C.
DR   InterPro; IPR022657; De-COase2_CS.
DR   InterPro; IPR022644; De-COase2_N.
DR   InterPro; IPR022653; De-COase2_pyr-phos_BS.
DR   InterPro; IPR000183; Orn/DAP/Arg_de-COase.
DR   InterPro; IPR029066; PLP-binding_barrel.
DR   Pfam; PF02784; Orn_Arg_deC_N; 1.
DR   Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR   PRINTS; PR01181; DAPDCRBXLASE.
DR   PRINTS; PR01179; ODADCRBXLASE.
DR   SUPFAM; SSF50621; SSF50621; 1.
DR   SUPFAM; SSF51419; SSF51419; 1.
DR   TIGRFAMs; TIGR01048; lysA; 1.
DR   PROSITE; PS00878; ODR_DC_2_1; 1.
DR   PROSITE; PS00879; ODR_DC_2_2; 1.
PE   2: Evidence at transcript level;
KW   Amino-acid biosynthesis; Chloroplast; Decarboxylase; Lyase;
KW   Lysine biosynthesis; Plastid; Pyridoxal phosphate; Reference proteome;
KW   Transit peptide.
FT   TRANSIT         1..44
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           45..490
FT                   /note="Probable diaminopimelate decarboxylase,
FT                   chloroplastic"
FT                   /id="PRO_0000307178"
FT   REGION          45..66
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        415
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255"
FT   BINDING         309
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000250"
FT   BINDING         345..348
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000250"
FT   BINDING         348
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         384
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         388
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         416
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         444
FT                   /ligand="pyridoxal 5'-phosphate"
FT                   /ligand_id="ChEBI:CHEBI:597326"
FT                   /evidence="ECO:0000250"
FT   BINDING         444
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   MOD_RES         130
FT                   /note="N6-(pyridoxal phosphate)lysine"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   490 AA;  53215 MW;  AE85784ECEB0080C CRC64;
     MAAANLLSRA LLPALNPNPS SHSNRVSPSA VSLRCRHGLT ASVRASLSTA APSPPPRPAA
     AAADGRAPKR CFRRGADGHL YCEGVRVEDA MGAAERTPFY LYSKPQVVRN FTAYRDALEG
     LRSIVGYAVK ANNNLRVLQL LRELGCGAVL VSGNELRLAL RAGFDPTRCI FNGNGKTLED
     LVLAAESGVF VNIDSEFDLE NIVTAARVAG KKVPVLLRIN PDVDPQVHPY VATGNKTSKF
     GIRNEKLQWF LDSIKSYSND ITLVGVHCHL GSTITKVDIF RDAAGLMVNY VDEIRAQGFE
     LEYLNIGGGL GIDYHHTDAV LPTPMDLINT VRELVLSRDL TLIIEPGRSL IANTCCFVNR
     VTGVKSNGTK NFIVVDGSMA ELIRPSLYGA YQHIELVSPS PDAEVATFDI VGPVCESADF
     LGKDRELPTP DKGAGLVVHD AGAYCMSMAS TYNLKLRPPE YWVEDDGSIA KIRRGESFDD
     YMKFFDNLSA