ISPF_ORYSJ
ID ISPF_ORYSJ Reviewed; 222 AA.
AC Q6EPN6; A0A0N7KFV8; Q0DYN3;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic {ECO:0000305};
DE Short=MECDP-synthase {ECO:0000303|PubMed:17634747};
DE Short=MECPS {ECO:0000305};
DE Short=MECS {ECO:0000305};
DE EC=4.6.1.12 {ECO:0000305|PubMed:29143298};
DE Flags: Precursor;
GN Name=ISPF {ECO:0000303|PubMed:29143298};
GN Synonyms=MCS {ECO:0000303|PubMed:17634747};
GN OrderedLocusNames=Os02g0680600 {ECO:0000312|EMBL:BAS80297.1},
GN LOC_Os02g45660 {ECO:0000305};
GN ORFNames=P0663F07.27 {ECO:0000312|EMBL:BAD29384.1};
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=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 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).
RN [5]
RP INDUCTION.
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).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND
RP MUTAGENESIS OF LEU-117.
RX PubMed=29143298; DOI=10.1007/s11103-017-0668-7;
RA Huang R., Wang Y., Wang P., Li C., Xiao F., Chen N., Li N., Li C., Sun C.,
RA Li L., Chen R., Xu Z., Zhu J., Deng X.;
RT "A single nucleotide mutation of IspF gene involved in the MEP pathway for
RT isoprenoid biosynthesis causes yellow-green leaf phenotype in rice.";
RL Plant Mol. Biol. 96:5-16(2018).
CC -!- FUNCTION: Enzyme of the plastid non-mevalonate pathway for isoprenoid
CC biosynthesis that converts 4-diphosphocytidyl-2C-methyl-D-erythritol 2-
CC phosphate into 2C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP
CC (Probable). Is essential for chloroplast development (PubMed:29143298).
CC {ECO:0000269|PubMed:29143298, ECO:0000305|PubMed:29143298}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-
CC erythritol 2,4-cyclic diphosphate + CMP; Xref=Rhea:RHEA:23864,
CC ChEBI:CHEBI:57919, ChEBI:CHEBI:58483, ChEBI:CHEBI:60377; EC=4.6.1.12;
CC Evidence={ECO:0000305|PubMed:29143298};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:Q9CAK8};
CC Note=Binds 1 divalent metal cation per subunit.
CC {ECO:0000250|UniProtKB:Q9CAK8};
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC phosphate: step 4/6. {ECO:0000305}.
CC -!- SUBUNIT: Homotrimer. {ECO:0000250|UniProtKB:Q9CAK8}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:29143298}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems, leaf sheaths and
CC young panicles. {ECO:0000269|PubMed:29143298}.
CC -!- INDUCTION: Induced by jasmonate, copper, UV and chitin oligosaccharide
CC elicitor. {ECO:0000269|PubMed:17634747}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF09655.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAG87377.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=BAS80297.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP005823; BAD29384.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF09655.1; ALT_INIT; Genomic_DNA.
DR EMBL; AP014958; BAS80297.1; ALT_INIT; Genomic_DNA.
DR EMBL; AK060238; BAG87377.1; ALT_INIT; mRNA.
DR RefSeq; XP_015627624.1; XM_015772138.1.
DR AlphaFoldDB; Q6EPN6; -.
DR SMR; Q6EPN6; -.
DR STRING; 4530.OS02T0680600-01; -.
DR PaxDb; Q6EPN6; -.
DR EnsemblPlants; Os02t0680600-01; Os02t0680600-01; Os02g0680600.
DR GeneID; 4330320; -.
DR Gramene; Os02t0680600-01; Os02t0680600-01; Os02g0680600.
DR KEGG; osa:4330320; -.
DR eggNOG; ENOG502QS77; Eukaryota.
DR HOGENOM; CLU_084630_0_0_1; -.
DR InParanoid; Q6EPN6; -.
DR OrthoDB; 1516374at2759; -.
DR PlantReactome; R-OSA-1119464; Methylerythritol phosphate pathway.
DR UniPathway; UPA00056; UER00095.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR Genevisible; Q6EPN6; OS.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0008685; F:2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEA:UniProtKB-UniPathway.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:InterPro.
DR CDD; cd00554; MECDP_synthase; 1.
DR Gene3D; 3.30.1330.50; -; 1.
DR HAMAP; MF_00107; IspF; 1.
DR InterPro; IPR003526; MECDP_synthase.
DR InterPro; IPR020555; MECDP_synthase_CS.
DR InterPro; IPR036571; MECDP_synthase_sf.
DR PANTHER; PTHR43181; PTHR43181; 1.
DR Pfam; PF02542; YgbB; 1.
DR SUPFAM; SSF69765; SSF69765; 1.
DR TIGRFAMs; TIGR00151; ispF; 1.
DR PROSITE; PS01350; ISPF; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Isoprene biosynthesis; Lyase; Metal-binding; Plastid;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..43
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 44..222
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase, chloroplastic"
FT /id="PRO_0000417597"
FT BINDING 73..75
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 73
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 75
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 99..100
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 103..111
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 107
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 121..123
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 126..130
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 130
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 165..171
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 196..200
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT SITE 99
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT SITE 198
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT MUTAGEN 117
FT /note="L->F: In 505ys; yellow-green leaf phenotype, delayed
FT heading, and reduced seed-setting rate and grain weight."
FT /evidence="ECO:0000269|PubMed:29143298"
SQ SEQUENCE 222 AA; 23524 MW; E2177B22E4AFCC72 CRC64;
MATASSLFLA SPVATAPTAR ARSTPSASPA RPSLRLRRPS TLAAAAVQAE HQPAVAAAPK
PPALPFRVGH GFDLHRLEPG LPLIIGGIDI PHDRGCDAHS DGDVLLHCVV DAILGALGLP
DIGQIFPDSD PRWKGADSSV FMREAVKLMH EAGYELGNLD ATLILQKPKI SPFKETIRSN
LCDLLGADPS VVNLKAKTHE KVDSLGENRS IAAHTVVLLM RK
