DAPB2_ORYSJ
ID DAPB2_ORYSJ Reviewed; 325 AA.
AC Q10P67; A3AG10; B7ESW8; Q0DTI8; Q10P66;
DT 23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=Probable 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic;
DE Short=HTPA reductase 2;
DE EC=1.17.1.8;
DE Flags: Precursor;
GN Name=DAPB2; OrderedLocusNames=Os03g0245100, LOC_Os03g14120;
GN ORFNames=OsJ_009732, OsJ_10116 {ECO:0000312|EMBL:EEE58685.1};
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 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] (ISOFORMS 1 AND 2).
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: Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate
CC (HTPA) to tetrahydrodipicolinate. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-
CC hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH;
CC Xref=Rhea:RHEA:35323, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16845, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:67139; EC=1.17.1.8;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-
CC 4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH;
CC Xref=Rhea:RHEA:35331, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16845, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:67139; EC=1.17.1.8;
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q10P67-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q10P67-2; Sequence=VSP_028630;
CC -!- SIMILARITY: Belongs to the DapB family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a dihydrodipicolinate reductase
CC (DHDPR), catalyzing the conversion of dihydrodipicolinate to
CC tetrahydrodipicolinate. However, it was shown in E.coli that the
CC substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP)
CC but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid
CC (HTPA), the product released by the DapA-catalyzed reaction.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF11450.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; DP000009; ABF94935.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF94936.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF94937.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF11450.1; ALT_INIT; Genomic_DNA.
DR EMBL; AP014959; BAS83232.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS83233.1; -; Genomic_DNA.
DR EMBL; CM000140; EEE58685.1; -; Genomic_DNA.
DR EMBL; AK059346; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AK102253; BAG95465.1; -; mRNA.
DR RefSeq; XP_015631811.1; XM_015776325.1. [Q10P67-1]
DR AlphaFoldDB; Q10P67; -.
DR SMR; Q10P67; -.
DR STRING; 4530.OS03T0245100-01; -.
DR PaxDb; Q10P67; -.
DR PRIDE; Q10P67; -.
DR EnsemblPlants; Os03t0245100-01; Os03t0245100-01; Os03g0245100. [Q10P67-1]
DR EnsemblPlants; Os03t0245100-02; Os03t0245100-02; Os03g0245100. [Q10P67-2]
DR GeneID; 4332231; -.
DR Gramene; Os03t0245100-01; Os03t0245100-01; Os03g0245100. [Q10P67-1]
DR Gramene; Os03t0245100-02; Os03t0245100-02; Os03g0245100. [Q10P67-2]
DR KEGG; osa:4332231; -.
DR eggNOG; ENOG502QPSY; Eukaryota.
DR InParanoid; Q10P67; -.
DR OMA; MERMVKI; -.
DR OrthoDB; 1236470at2759; -.
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; UER00018.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR ExpressionAtlas; Q10P67; baseline and differential.
DR Genevisible; Q10P67; OS.
DR GO; GO:0009570; C:chloroplast stroma; IBA:GO_Central.
DR GO; GO:0008839; F:4-hydroxy-tetrahydrodipicolinate reductase; IBA:GO_Central.
DR GO; GO:0070402; F:NADPH binding; IEA:InterPro.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR InterPro; IPR022663; DapB_C.
DR InterPro; IPR000846; DapB_N.
DR InterPro; IPR023940; DHDPR_bac.
DR InterPro; IPR011859; Dihydrodipicolinate_Rdtase_pln.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR20836; PTHR20836; 1.
DR Pfam; PF05173; DapB_C; 1.
DR Pfam; PF01113; DapB_N; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR02130; dapB_plant; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Amino-acid biosynthesis; Chloroplast;
KW Diaminopimelate biosynthesis; Lysine biosynthesis; NAD; NADP;
KW Oxidoreductase; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..32
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 33..325
FT /note="Probable 4-hydroxy-tetrahydrodipicolinate reductase
FT 2, chloroplastic"
FT /id="PRO_0000307186"
FT ACT_SITE 208
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 212
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 57..62
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 149..151
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 172..175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250"
FT BINDING 217..218
FT /ligand="(S)-2,3,4,5-tetrahydrodipicolinate"
FT /ligand_id="ChEBI:CHEBI:16845"
FT /evidence="ECO:0000250"
FT VAR_SEQ 179..203
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_028630"
SQ SEQUENCE 325 AA; 35574 MW; E1A4D87189A0585F CRC64;
MLSLRPPCTL SPAPWRRRRT LHGAAGTPQR VSVAAPSAIV EAVSPPARFS FPILVNGCTG
KMGLSVAEAV TSSGLHLVPI SFSSRDTLDR TVRVGHTDVR IYGPSAREDV LSSVIDEFPD
VVVVDYTAPD SVNANAELYC KLGLPFVMGT TGGDRQLLYK SVQDSNNYAL ISPQMGKQVV
AFLAAMEIMA EQFPGAFSGY HLEVLESHQA GKLDISGTAK AVIACFEKLG VSYDMNRMVK
IRDPEQQLEM VGVPEEHIEG HAFHLYHLTS PDDSVSFEFQ HNVCGRSIYA EGSVDAAMFL
HRKVRSNDSK RIYDMIDVLR EGSMR
