ISPF_ARATH
ID ISPF_ARATH Reviewed; 231 AA.
AC Q9CAK8; Q8LE87; Q9GDE3; Q9SH48;
DT 17-JAN-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic {ECO:0000305};
DE Short=MECDP-synthase {ECO:0000312|EMBL:AAG35071.1};
DE Short=MECPS {ECO:0000305};
DE Short=MECS {ECO:0000305};
DE EC=4.6.1.12 {ECO:0000305|PubMed:16231155};
DE Flags: Precursor;
GN Name=ISPF {ECO:0000303|PubMed:16231155};
GN Synonyms=MCS {ECO:0000303|PubMed:17660251}, MDS {ECO:0000305};
GN OrderedLocusNames=At1g63970 {ECO:0000312|Araport:AT1G63970};
GN ORFNames=F22C12.26 {ECO:0000312|EMBL:AAF24570.1},
GN T12P18.1 {ECO:0000312|EMBL:AAG52445.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
RA Rohdich F.;
RT "2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Arabidopsis
RT thaliana.";
RL Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP INDUCTION.
RX PubMed=15863698; DOI=10.1104/pp.104.058735;
RA Hsieh M.H., Goodman H.M.;
RT "The Arabidopsis IspH homolog is involved in the plastid nonmevalonate
RT pathway of isoprenoid biosynthesis.";
RL Plant Physiol. 138:641-653(2005).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RX PubMed=16231155; DOI=10.1007/s00425-005-0140-9;
RA Hsieh M.H., Goodman H.M.;
RT "Functional evidence for the involvement of Arabidopsis IspF homolog in the
RT nonmevalonate pathway of plastid isoprenoid biosynthesis.";
RL Planta 223:779-784(2006).
RN [8]
RP SUBCELLULAR LOCATION.
RX PubMed=18236010; DOI=10.1007/s11103-008-9297-5;
RA Hsieh M.H., Chang C.Y., Hsu S.J., Chen J.J.;
RT "Chloroplast localization of methylerythritol 4-phosphate pathway enzymes
RT and regulation of mitochondrial genes in ispD and ispE albino mutants in
RT Arabidopsis.";
RL Plant Mol. Biol. 66:663-673(2008).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 72-231 IN COMPLEX WITH CMP AND
RP ZINC IONS, SUBUNIT, AND COFACTOR.
RX PubMed=17660251; DOI=10.1110/ps.072972807;
RA Calisto B.M., Perez-Gil J., Bergua M., Querol-Audi J., Fita I.,
RA Imperial S.;
RT "Biosynthesis of isoprenoids in plants: structure of the 2C-methyl-D-
RT erithrytol 2,4-cyclodiphosphate synthase from Arabidopsis thaliana.
RT Comparison with the bacterial enzymes.";
RL Protein Sci. 16:2082-2088(2007).
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. Is
CC essential for chloroplast development. {ECO:0000269|PubMed:16231155}.
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:16231155};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|PubMed:17660251};
CC Note=Binds 1 divalent metal cation per subunit.
CC {ECO:0000269|PubMed:17660251};
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:0000269|PubMed:17660251}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000305|PubMed:18236010}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9CAK8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9CAK8-2; Sequence=VSP_009112;
CC -!- INDUCTION: Circadian-regulated with a peak in the late period of dark
CC phase and early period of the light phase.
CC {ECO:0000269|PubMed:15863698}.
CC -!- DISRUPTION PHENOTYPE: Albino phenotype and seedling lethal when
CC homozygous. The phenotype is caused by an early arrest in chloroplast
CC differentiation. {ECO:0000269|PubMed:16231155}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the IspF family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF24570.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF321531; AAG35071.1; -; mRNA.
DR EMBL; AC007764; AAF24570.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC010852; AAG52445.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE34174.1; -; Genomic_DNA.
DR EMBL; AY059096; AAL15202.1; -; mRNA.
DR EMBL; AF370154; AAK43969.1; -; mRNA.
DR EMBL; AY085564; AAM62786.1; -; mRNA.
DR PIR; H96664; H96664.
DR RefSeq; NP_001319313.1; NM_001334142.1.
DR RefSeq; NP_850971.1; NM_180640.3. [Q9CAK8-1]
DR PDB; 2PMP; X-ray; 2.30 A; A=72-231.
DR PDBsum; 2PMP; -.
DR AlphaFoldDB; Q9CAK8; -.
DR SMR; Q9CAK8; -.
DR BioGRID; 27921; 5.
DR IntAct; Q9CAK8; 6.
DR STRING; 3702.AT1G63970.1; -.
DR BindingDB; Q9CAK8; -.
DR ChEMBL; CHEMBL2285351; -.
DR PaxDb; Q9CAK8; -.
DR PRIDE; Q9CAK8; -.
DR ProteomicsDB; 250683; -. [Q9CAK8-1]
DR EnsemblPlants; AT1G63970.1; AT1G63970.1; AT1G63970. [Q9CAK8-1]
DR GeneID; 842700; -.
DR Gramene; AT1G63970.1; AT1G63970.1; AT1G63970. [Q9CAK8-1]
DR KEGG; ath:AT1G63970; -.
DR Araport; AT1G63970; -.
DR TAIR; locus:2024618; AT1G63970.
DR eggNOG; ENOG502QS77; Eukaryota.
DR HOGENOM; CLU_084630_0_1_1; -.
DR InParanoid; Q9CAK8; -.
DR OMA; QHFGTGR; -.
DR OrthoDB; 1516374at2759; -.
DR PhylomeDB; Q9CAK8; -.
DR BioCyc; ARA:AT1G63970-MON; -.
DR BioCyc; MetaCyc:AT1G63970-MON; -.
DR BRENDA; 4.6.1.12; 399.
DR SABIO-RK; Q9CAK8; -.
DR UniPathway; UPA00056; UER00095.
DR EvolutionaryTrace; Q9CAK8; -.
DR PRO; PR:Q9CAK8; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9CAK8; baseline and differential.
DR Genevisible; Q9CAK8; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
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:0016117; P:carotenoid biosynthetic process; IMP:TAIR.
DR GO; GO:0015995; P:chlorophyll biosynthetic process; IMP:TAIR.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEA:UniProtKB-UniPathway.
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 3D-structure; Alternative splicing; Chloroplast; Isoprene biosynthesis;
KW Lyase; Metal-binding; Plastid; Reference proteome; Transit peptide.
FT TRANSIT 1..52
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 53..231
FT /note="2-C-methyl-D-erythritol 2,4-cyclodiphosphate
FT synthase, chloroplastic"
FT /id="PRO_0000016482"
FT BINDING 82..84
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 82
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0007744|PDB:2PMP"
FT BINDING 84
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:17660251,
FT ECO:0007744|PDB:2PMP"
FT BINDING 108..109
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 112..120
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 116
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:17660251,
FT ECO:0007744|PDB:2PMP"
FT BINDING 130..132
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17660251,
FT ECO:0007744|PDB:2PMP"
FT BINDING 135..139
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 139
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT BINDING 174..180
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17660251,
FT ECO:0007744|PDB:2PMP"
FT BINDING 205..209
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT SITE 108
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT SITE 207
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P62617"
FT VAR_SEQ 111..118
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.1"
FT /id="VSP_009112"
FT CONFLICT 98
FT /note="V -> D (in Ref. 1; AAG35071 and 5; AAM62786)"
FT /evidence="ECO:0000305"
FT CONFLICT 144
FT /note="G -> E (in Ref. 1; AAG35071)"
FT /evidence="ECO:0000305"
FT CONFLICT 166
FT /note="G -> A (in Ref. 5; AAM62786)"
FT /evidence="ECO:0000305"
FT CONFLICT 220
FT /note="I -> V (in Ref. 1; AAG35071)"
FT /evidence="ECO:0000305"
FT STRAND 74..88
FT /evidence="ECO:0007829|PDB:2PMP"
FT STRAND 102..105
FT /evidence="ECO:0007829|PDB:2PMP"
FT STRAND 107..109
FT /evidence="ECO:0007829|PDB:2PMP"
FT HELIX 113..126
FT /evidence="ECO:0007829|PDB:2PMP"
FT HELIX 131..134
FT /evidence="ECO:0007829|PDB:2PMP"
FT HELIX 147..161
FT /evidence="ECO:0007829|PDB:2PMP"
FT STRAND 163..173
FT /evidence="ECO:0007829|PDB:2PMP"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:2PMP"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:2PMP"
FT HELIX 183..194
FT /evidence="ECO:0007829|PDB:2PMP"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:2PMP"
FT STRAND 201..206
FT /evidence="ECO:0007829|PDB:2PMP"
FT HELIX 212..215
FT /evidence="ECO:0007829|PDB:2PMP"
FT STRAND 218..230
FT /evidence="ECO:0007829|PDB:2PMP"
SQ SEQUENCE 231 AA; 24812 MW; 8E5DD02EC7E2FD44 CRC64;
MATSSTQLLL SSSSLFHSQI TKKPFLLPAT KIGVWRPKKS LSLSCRPSAS VSAASSAVDV
NESVTSEKPT KTLPFRIGHG FDLHRLEPGY PLIIGGIVIP HDRGCEAHSD GDVLLHCVVD
AILGALGLPD IGQIFPDSDP KWKGAASSVF IKEAVRLMDE AGYEIGNLDA TLILQRPKIS
PHKETIRSNL SKLLGADPSV VNLKAKTHEK VDSLGENRSI AAHTVILLMK K
