NCED3_ORYSJ
ID NCED3_ORYSJ Reviewed; 608 AA.
AC Q5MBR5;
DT 05-JUL-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=9-cis-epoxycarotenoid dioxygenase NCED3, chloroplastic {ECO:0000305};
DE Short=OsNCED3 {ECO:0000312|EMBL:AAW21319.1};
DE EC=1.13.11.51 {ECO:0000250|UniProtKB:O24592};
DE Flags: Precursor;
GN Name=NCED3 {ECO:0000312|EMBL:AAW21319.1};
GN OrderedLocusNames=Os03g0645900 {ECO:0000312|EMBL:BAF12679.1},
GN LOC_Os03g44380 {ECO:0000312|EMBL:ABF97874.1};
GN ORFNames=OsJ_11896 {ECO:0000312|EMBL:EAZ27934.1};
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 [MRNA].
RA Dian W.M.;
RT "Oryza sativa japonica group 9-cis-epoxycarotenoid dioxygenase 3 (NCED3)
RT mRNA.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
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 INDUCTION.
RX PubMed=17205969; DOI=10.1093/pcp/pcm003;
RA Saika H., Okamoto M., Miyoshi K., Kushiro T., Shinoda S., Jikumaru Y.,
RA Fujimoto M., Arikawa T., Takahashi H., Ando M., Arimura S., Miyao A.,
RA Hirochika H., Kamiya Y., Tsutsumi N., Nambara E., Nakazono M.;
RT "Ethylene promotes submergence-induced expression of OsABA8ox1, a gene that
RT encodes ABA 8'-hydroxylase in rice.";
RL Plant Cell Physiol. 48:287-298(2007).
RN [8]
RP INDUCTION.
RX PubMed=18326788; DOI=10.1104/pp.108.117028;
RA Welsch R., Wuest F., Baer C., Al-Babili S., Beyer P.;
RT "A third phytoene synthase is devoted to abiotic stress-induced abscisic
RT acid formation in rice and defines functional diversification of phytoene
RT synthase genes.";
RL Plant Physiol. 147:367-380(2008).
RN [9]
RP INDUCTION BY DROUGHT STRESS.
RX PubMed=20838584; DOI=10.1371/journal.pgen.1001098;
RA Yaish M.W., El-Kereamy A., Zhu T., Beatty P.H., Good A.G., Bi Y.M.,
RA Rothstein S.J.;
RT "The APETALA-2-like transcription factor OsAP2-39 controls key interactions
RT between abscisic acid and gibberellin in rice.";
RL PLoS Genet. 6:E1001098-E1001098(2010).
RN [10]
RP TISSUE SPECIFICITY.
RX PubMed=21502188; DOI=10.1104/pp.111.176164;
RA Ji X., Dong B., Shiran B., Talbot M.J., Edlington J.E., Hughes T.,
RA White R.G., Gubler F., Dolferus R.;
RT "Control of abscisic acid catabolism and abscisic acid homeostasis is
RT important for reproductive stage stress tolerance in cereals.";
RL Plant Physiol. 156:647-662(2011).
RN [11]
RP INDUCTION BY D-ALLOSE.
RX PubMed=23397192; DOI=10.1007/s00425-013-1853-9;
RA Fukumoto T., Kano A., Ohtani K., Inoue M., Yoshihara A., Izumori K.,
RA Tajima S., Shigematsu Y., Tanaka K., Ohkouchi T., Ishida Y., Nishizawa Y.,
RA Tada Y., Ichimura K., Gomi K., Yoo S.D., Sheen J., Akimitsu K.;
RT "Phosphorylation of D-allose by hexokinase involved in regulation of OsABF1
RT expression for growth inhibition in Oryza sativa L.";
RL Planta 237:1379-1391(2013).
RN [12]
RP INDUCTION BY INFECTION WITH XOO.
RX PubMed=23826294; DOI=10.1371/journal.pone.0067413;
RA Xu J., Audenaert K., Hofte M., De Vleesschauwer D.;
RT "Abscisic acid promotes susceptibility to the rice leaf blight pathogen
RT Xanthomonas oryzae pv oryzae by suppressing salicylic acid-mediated
RT defenses.";
RL PLoS ONE 8:E67413-E67413(2013).
RN [13]
RP INDUCTION BY DROUGHT STRESS.
RX PubMed=25418692; DOI=10.1111/jipb.12313;
RA Du H., Chang Y., Huang F., Xiong L.;
RT "GID1 modulates stomatal response and submergence tolerance involving
RT abscisic acid and gibberellic acid signaling in rice.";
RL J. Integr. Plant Biol. 57:954-968(2015).
RN [14]
RP INDUCTION.
RX PubMed=25283804; DOI=10.1111/pbi.12270;
RA Chen M., Zhao Y., Zhuo C., Lu S., Guo Z.;
RT "Overexpression of a NF-YC transcription factor from bermudagrass confers
RT tolerance to drought and salinity in transgenic rice.";
RL Plant Biotechnol. J. 13:482-491(2015).
RN [15]
RP INDUCTION BY DROUGHT STRESS.
RX PubMed=25735958; DOI=10.1093/pcp/pcv022;
RA Shi L., Guo M., Ye N., Liu Y., Liu R., Xia Y., Cui S., Zhang J.;
RT "Reduced ABA accumulation in the root system is caused by ABA exudation in
RT upland rice (Oryza sativa L. var. Gaoshan1) and this enhanced drought
RT adaptation.";
RL Plant Cell Physiol. 56:951-964(2015).
RN [16]
RP INDUCTION BY INFECTION WITH XOO.
RX PubMed=26718470; DOI=10.4014/jmb.1510.10072;
RA Li S.B., Xu S.R., Zhang R.N., Liu Y., Zhou R.C.;
RT "The antibiosis action and rice-induced resistance, mediated by a
RT lipopeptide from Bacillus amyloliquefaciens B014, in controlling rice
RT disease caused by Xanthomonas oryzae pv. oryzae.";
RL J. Microbiol. Biotechnol. 26:748-756(2016).
CC -!- FUNCTION: Has a 11,12(11',12') 9-cis epoxycarotenoid cleavage activity.
CC Catalyzes the first step of abscisic-acid biosynthesis from
CC carotenoids. {ECO:0000250|UniProtKB:O24592}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 9-cis-epoxycarotenoid + O2 = 2-cis,4-trans-xanthoxin + a
CC 12'-apo-carotenal; Xref=Rhea:RHEA:23328, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:32304, ChEBI:CHEBI:51972, ChEBI:CHEBI:51973;
CC EC=1.13.11.51; Evidence={ECO:0000250|UniProtKB:O24592};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=9-cis-violaxanthin + O2 = (3S,5R,6S)-5,6-epoxy-3-hydroxy-5,6-
CC dihydro-12'-apo-beta-caroten-12'-al + 2-cis,4-trans-xanthoxin;
CC Xref=Rhea:RHEA:16541, ChEBI:CHEBI:15379, ChEBI:CHEBI:32304,
CC ChEBI:CHEBI:34597, ChEBI:CHEBI:35305; EC=1.13.11.51;
CC Evidence={ECO:0000250|UniProtKB:O24592};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=9'-cis-neoxanthin + O2 = (3S,5R,6R)-3,5-dihydroxy-6,7-
CC didehydro-5,6-dihydro-12'-apo-beta-caroten-12'-al + 2-cis,4-trans-
CC xanthoxin; Xref=Rhea:RHEA:19677, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:32304, ChEBI:CHEBI:34596, ChEBI:CHEBI:35306;
CC EC=1.13.11.51; Evidence={ECO:0000250|UniProtKB:O24592};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:O24592};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:O24592};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255}.
CC -!- TISSUE SPECIFICITY: Expressed in vascular bundles of roots and leaves,
CC vascular parenchyma cells of leaves, anther filaments, xylem tissue of
CC anthers, embryos, radicles and coleoptiles.
CC {ECO:0000269|PubMed:21502188}.
CC -!- INDUCTION: Induced by abscisic acid (ABA) and salt (PubMed:18326788,
CC PubMed:25283804). Induced by drought stress (PubMed:20838584,
CC PubMed:25418692, PubMed:25283804, PubMed:25735958). Induced by D-allose
CC (PubMed:23397192). Induced by infection with the bacterial pathogen
CC Xanthomonas oryzae pv. oryzae (Xoo) (PubMed:23826294, PubMed:26718470).
CC Down-regulated by submergence (PubMed:17205969).
CC {ECO:0000269|PubMed:17205969, ECO:0000269|PubMed:18326788,
CC ECO:0000269|PubMed:20838584, ECO:0000269|PubMed:23397192,
CC ECO:0000269|PubMed:23826294, ECO:0000269|PubMed:25283804,
CC ECO:0000269|PubMed:25418692, ECO:0000269|PubMed:25735958,
CC ECO:0000269|PubMed:26718470}.
CC -!- SIMILARITY: Belongs to the carotenoid oxygenase family. {ECO:0000305}.
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DR EMBL; AY838899; AAW21319.1; -; mRNA.
DR EMBL; DP000009; ABF97874.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF12679.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS85471.1; -; Genomic_DNA.
DR EMBL; CM000140; EAZ27934.1; -; Genomic_DNA.
DR RefSeq; XP_015631538.1; XM_015776052.1.
DR AlphaFoldDB; Q5MBR5; -.
DR SMR; Q5MBR5; -.
DR STRING; 4530.OS03T0645900-00; -.
DR PaxDb; Q5MBR5; -.
DR PRIDE; Q5MBR5; -.
DR EnsemblPlants; Os03t0645900-00; Os03t0645900-00; Os03g0645900.
DR GeneID; 4333566; -.
DR Gramene; Os03t0645900-00; Os03t0645900-00; Os03g0645900.
DR KEGG; osa:4333566; -.
DR eggNOG; KOG1285; Eukaryota.
DR HOGENOM; CLU_016472_0_0_1; -.
DR InParanoid; Q5MBR5; -.
DR OMA; SYRNRWV; -.
DR OrthoDB; 524712at2759; -.
DR PlantReactome; R-OSA-1119374; Abscisic acid biosynthesis.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000007752; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR GO; GO:0009570; C:chloroplast stroma; IBA:GO_Central.
DR GO; GO:0045549; F:9-cis-epoxycarotenoid dioxygenase activity; IEA:UniProtKB-EC.
DR GO; GO:0010436; F:carotenoid dioxygenase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009688; P:abscisic acid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0016121; P:carotene catabolic process; IBA:GO_Central.
DR InterPro; IPR004294; Carotenoid_Oase.
DR PANTHER; PTHR10543; PTHR10543; 1.
DR Pfam; PF03055; RPE65; 1.
PE 2: Evidence at transcript level;
KW Abscisic acid biosynthesis; Chloroplast; Dioxygenase; Iron; Metal-binding;
KW Oxidoreductase; Plastid; Reference proteome; Stress response;
KW Transit peptide.
FT TRANSIT 1..38
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 39..608
FT /note="9-cis-epoxycarotenoid dioxygenase NCED3,
FT chloroplastic"
FT /id="PRO_0000440939"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 303
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
FT BINDING 352
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
FT BINDING 417
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
FT BINDING 595
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000250|UniProtKB:O24592"
SQ SEQUENCE 608 AA; 65651 MW; 39FF36DB440D4110 CRC64;
MATITTPGYA HIQRQHGRCS TTAGRRGASN SVRFSARAVS SVPHAAAASS APAFLPVPFV
PGADAPSPSG KSAIGVPKAP RKGEEGKRLN FFQRAAAMAL DAFEEGFVAN VLERPHGLPS
TADPAVQIAG NFAPVGETPP ARALPVSGRI PPFINGVYAR NGANPHFDPV AGHHLFDGDG
MVHAVRIRNG AAESYACRFT ETARLRQERA MGRPMFPKAI GELHGHSGIA RLALFYARAA
CGLLDPSHGT GVANAGLIYF NGRLLAMSED DLPYQVRVTA DGDLETVGRY DFDGQLGCAM
IAHPKLDPAT GELHALSYDV IKKPYLKYFY FAPDGTKSAD VEIPLDQPTM IHDFAITENY
VVVPDHQVVF KLQEMLRGGS PVVLDKEKTS RFGVLPKHAA DASEMVWVDV PDCFCFHLWN
AWEEADTDEV VVIGSCMTPA DSIFNESDDR LESVLTEIRL NTRTGESTRR AILPPSSQVN
LEVGMVNRNL LGRKTRYAYL AVAEPWPKVS GFAKVDLATG ELTKFEYGEG RFGGEPCFVP
MDAAAATPRG EDDGYILSFV HDERAGTSEL LVVNAADMRL EATVQLPSRV PYGFHGTFIT
GDELTTQA
