ISPD_ORYSJ
ID ISPD_ORYSJ Reviewed; 297 AA.
AC Q5N8G1; A4PIB9; C7IXL0;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic;
DE EC=2.7.7.60;
DE AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase;
DE Short=OsCMS;
DE AltName: Full=MEP cytidylyltransferase;
DE Flags: Precursor;
GN Name=ISPD; Synonyms=CMS; OrderedLocusNames=Os01g0887000, LOC_Os01g66360;
GN ORFNames=OsJ_04342, P0408G07.39, P0434C04.18;
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=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
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 [MRNA] OF 92-297.
RX PubMed=17634747; DOI=10.1007/s11103-007-9207-2;
RA Okada A., Shimizu T., Okada K., Kuzuyama T., Koga J., Shibuya N.,
RA Nojiri H., Yamane H.;
RT "Elicitor induced activation of the methylerythritol phosphate pathway
RT toward phytoalexins biosynthesis in rice.";
RL Plant Mol. Biol. 65:177-187(2007).
CC -!- FUNCTION: Enzyme of the plastid non-mevalonate pathway for isoprenoid
CC biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-
CC methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate
CC (MEP). Is essential for chloroplast development (By similarity).
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-
CC methyl-D-erythritol + diphosphate; Xref=Rhea:RHEA:13429,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:33019, ChEBI:CHEBI:37563,
CC ChEBI:CHEBI:57823, ChEBI:CHEBI:58262; EC=2.7.7.60;
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC phosphate: step 2/6.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the IspD/TarI cytidylyltransferase family. IspD
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAH91416.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP003346; BAD82130.1; -; Genomic_DNA.
DR EMBL; AP003379; BAD82245.1; -; Genomic_DNA.
DR EMBL; AP008207; BAH91416.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014957; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000138; EAZ14419.1; -; Genomic_DNA.
DR EMBL; AB296384; BAF52631.1; -; mRNA.
DR RefSeq; XP_015625415.1; XM_015769929.1.
DR RefSeq; XP_015626188.1; XM_015770702.1.
DR AlphaFoldDB; Q5N8G1; -.
DR SMR; Q5N8G1; -.
DR STRING; 4530.OS01T0887100-01; -.
DR PaxDb; Q5N8G1; -.
DR PRIDE; Q5N8G1; -.
DR GeneID; 9266653; -.
DR KEGG; osa:9266653; -.
DR eggNOG; ENOG502QUUE; Eukaryota.
DR HOGENOM; CLU_061281_0_0_1; -.
DR InParanoid; Q5N8G1; -.
DR OrthoDB; 1356473at2759; -.
DR PlantReactome; R-OSA-1119464; Methylerythritol phosphate pathway.
DR UniPathway; UPA00056; UER00093.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000007752; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR GO; GO:0050518; F:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity; IBA:GO_Central.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEA:UniProtKB-UniPathway.
DR CDD; cd02516; CDP-ME_synthetase; 1.
DR Gene3D; 3.90.550.10; -; 1.
DR HAMAP; MF_00108; IspD; 1.
DR InterPro; IPR001228; IspD.
DR InterPro; IPR034683; IspD/TarI.
DR InterPro; IPR018294; ISPD_synthase_CS.
DR InterPro; IPR029044; Nucleotide-diphossugar_trans.
DR Pfam; PF01128; IspD; 1.
DR SUPFAM; SSF53448; SSF53448; 1.
DR TIGRFAMs; TIGR00453; ispD; 1.
DR PROSITE; PS01295; ISPD; 1.
PE 2: Evidence at transcript level;
KW Chloroplast; Isoprene biosynthesis; Nucleotidyltransferase; Plastid;
KW Reference proteome; Transferase; Transit peptide.
FT TRANSIT 1..57
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 58..297
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase, chloroplastic"
FT /id="PRO_0000417595"
FT SITE 87
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT SITE 94
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT SITE 224
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000250"
FT SITE 280
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000250"
SQ SEQUENCE 297 AA; 32464 MW; 3E2496C84D040274 CRC64;
MELRLCLRLH APPASAPTTH PPPPLSPSPN LALRRLRTGG SCAVAPRRHA RKWGSAVCAA
KADGAQGEAV KERSVSVVLL SGGQGKRMGA SMPKQYLPLL GLPIALHSLK TFCQLKEVKE
VVVVCDPDYK DIFEGSIENV QIPIKFALPG KERQDSVYNG LQEIDGDSEL VCVHDSARPL
VSSEDVKKVL EDAIVHGAAV LGVPVKATIK EADSNSFVVK TLDRKTLWEM QTPQVMRPSL
LRDGFELVKR DGLEVTDDVS IVEYLKHSVY ITEGSYTNIK VTTPDDLLLA ERLMNEK
