DAPAT_ORYSJ
ID DAPAT_ORYSJ Reviewed; 464 AA.
AC Q10MQ2; A0A0P0VWF4; Q10MQ1; Q6VMN8;
DT 18-APR-2012, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Probable LL-diaminopimelate aminotransferase, chloroplastic;
DE Short=DAP-AT;
DE Short=DAP-aminotransferase;
DE Short=LL-DAP-aminotransferase;
DE EC=2.6.1.83;
DE Flags: Precursor;
GN Name=AGD2; OrderedLocusNames=Os03g0299900, LOC_Os03g18810;
GN ORFNames=OsJ_27598;
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].
RX PubMed=14729919; DOI=10.1105/tpc.019372;
RA Song J.T., Lu H., Greenberg J.T.;
RT "Divergent roles in Arabidopsis thaliana development and defense of two
RT homologous genes, aberrant growth and death2 and AGD2-LIKE DEFENSE RESPONSE
RT PROTEIN1, encoding novel aminotransferases.";
RL Plant Cell 16:353-366(2004).
RN [2]
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 [3]
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 [4]
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 [5]
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 [6]
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 [7]
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: Required for lysine biosynthesis. Catalyzes the direct
CC conversion of tetrahydrodipicolinate to LL-diaminopimelate, a reaction
CC that requires three enzymes in E.coli (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S,6S)-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-
CC 2,3,4,5-tetrahydrodipicolinate + H(+) + H2O + L-glutamate;
CC Xref=Rhea:RHEA:23988, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16845, ChEBI:CHEBI:29985,
CC ChEBI:CHEBI:57609; EC=2.6.1.83;
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; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate
CC (aminotransferase route): step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the class-I pyridoxal-phosphate-dependent
CC aminotransferase family. LL-diaminopimelate aminotransferase subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABF95474.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY338235; AAR01225.1; -; mRNA.
DR EMBL; DP000009; ABF95473.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF95474.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008209; BAF11766.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS83755.1; -; Genomic_DNA.
DR EMBL; CM000145; EEE68826.1; -; Genomic_DNA.
DR EMBL; AK069075; BAG91242.1; -; mRNA.
DR RefSeq; XP_015631441.1; XM_015775955.1.
DR AlphaFoldDB; Q10MQ2; -.
DR SMR; Q10MQ2; -.
DR STRING; 4530.OS03T0299900-01; -.
DR PaxDb; Q10MQ2; -.
DR PRIDE; Q10MQ2; -.
DR EnsemblPlants; Os03t0299900-01; Os03t0299900-01; Os03g0299900.
DR GeneID; 4332563; -.
DR Gramene; Os03t0299900-01; Os03t0299900-01; Os03g0299900.
DR KEGG; osa:4332563; -.
DR eggNOG; KOG0257; Eukaryota.
DR HOGENOM; CLU_051433_0_0_1; -.
DR InParanoid; Q10MQ2; -.
DR OMA; DFQARGC; -.
DR OrthoDB; 683031at2759; -.
DR PlantReactome; R-OSA-1119419; Lysine biosynthesis VI.
DR UniPathway; UPA00034; UER00466.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q10MQ2; OS.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0010285; F:L,L-diaminopimelate aminotransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:InterPro.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR HAMAP; MF_01642; DapL_aminotrans_1; 1.
DR InterPro; IPR004839; Aminotransferase_I/II.
DR InterPro; IPR019942; DapL/ALD1.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR PANTHER; PTHR43144; PTHR43144; 1.
DR Pfam; PF00155; Aminotran_1_2; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR TIGRFAMs; TIGR03542; DAPAT_plant; 1.
PE 2: Evidence at transcript level;
KW Aminotransferase; Chloroplast; Plastid; Pyridoxal phosphate;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..39
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 40..464
FT /note="Probable LL-diaminopimelate aminotransferase,
FT chloroplastic"
FT /id="PRO_0000416861"
FT BINDING 102
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 132
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250"
FT BINDING 135
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250"
FT BINDING 167
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 190
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 247
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 247
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 275
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 278
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 305
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 307
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 316
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT BINDING 347
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250"
FT BINDING 442
FT /ligand="substrate"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250"
FT MOD_RES 308
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT CONFLICT 8
FT /note="G -> A (in Ref. 1; AAR01225)"
FT /evidence="ECO:0000305"
FT CONFLICT 118
FT /note="K -> E (in Ref. 1; AAR01225)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 464 AA; 49858 MW; 57F9B88788D75B75 CRC64;
MAASPAAGAA AATVSSFVSP SSFSSVKASK PDRLRPARRA AAVNVRCVSS PPATETSFKT
KVPRNANMAK LQAGYLFPEI ARRRAAHLLK FPDAKIISLG IGDTTEPIPD VITNAMAKRA
HALSTVDGYS GYGAEQGEKK LRAAIAATYY ADLGIEETDI FVSDGAKCDI SRLQVLFGSN
VKIAVQDPSY PAYVDSSVIM GQTGLYQEDV QKYGNIEYMK CSPENGFFPD LSSVPRTDII
FFCSPNNPTG AAASRDQLTK LVKFAKDNGS IIVYDSAYAM YISDDSPKSI FEIPGAKEVA
IETASFSKYA GFTGVRLGWT VVPKELLFSD GHPVAKDFNR IVCTCFNGAS NISQAGGLGC
LSPEGLKAMS DVVGFYKENT KIIVDTFTSL GFNVYGAKNA PYVWVHFPGR NSWDVFAEIL
EKAHVVTTPG SGFGPGGEGF VRVSAFGHRE NIIEAARRLK QLYK
