ISPD_ARATH
ID ISPD_ARATH Reviewed; 302 AA.
AC P69834; O64726; Q9LL91;
DT 24-MAY-2005, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic;
DE EC=2.7.7.60 {ECO:0000269|PubMed:10841550};
DE AltName: Full=4-diphosphocytidyl-2C-methyl-D-erythritol synthase;
DE AltName: Full=MEP cytidylyltransferase;
DE Short=AtMECT;
DE Short=AtMEPCT;
DE Flags: Precursor;
GN Name=ISPD; Synonyms=MCT, MECT, MEPCT; OrderedLocusNames=At2g02500;
GN ORFNames=T8K22.20;
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], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RC STRAIN=cv. Columbia;
RX PubMed=10841550; DOI=10.1073/pnas.97.12.6451;
RA Rohdich F., Wungsintaweekul J., Eisenreich W., Richter G., Schuhr C.A.,
RA Hecht S., Zenk M.H., Bacher A.;
RT "Biosynthesis of terpenoids: 4-diphosphocytidyl-2C-methyl-D-erythritol
RT synthase of Arabidopsis thaliana.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:6451-6456(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=12029484; DOI=10.1007/s00425-002-0762-0;
RA Okada K., Kawaide H., Kuzuyama T., Seto H., Curtis I.S., Kamiya Y.;
RT "Antisense and chemical suppression of the nonmevalonate pathway affects
RT ent-kaurene biosynthesis in Arabidopsis.";
RL Planta 215:339-344(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 [7]
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 [8]
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION, AND
RP DISRUPTION PHENOTYPE.
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 ACETYLATION [LARGE SCALE ANALYSIS] AT SER-62, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER CYS-61, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 76-302, AND COFACTOR.
RX PubMed=16478479; DOI=10.1111/j.1742-4658.2006.05133.x;
RA Gabrielsen M., Kaiser J., Rohdich F., Eisenreich W., Laupitz R., Bacher A.,
RA Bond C.S., Hunter W.N.;
RT "The crystal structure of a plant 2C-methyl-D-erythritol 4-phosphate
RT cytidylyltransferase exhibits a distinct quaternary structure compared to
RT bacterial homologues and a possible role in feedback regulation for
RT cytidine monophosphate.";
RL FEBS J. 273:1065-1073(2006).
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 and required for
CC pigments and gibberellins biosynthesis. {ECO:0000269|PubMed:10841550,
CC ECO:0000269|PubMed:12029484, ECO:0000269|PubMed:18236010}.
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 Evidence={ECO:0000269|PubMed:10841550};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:13430;
CC Evidence={ECO:0000269|PubMed:10841550};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:10841550, ECO:0000269|PubMed:16478479};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:10841550, ECO:0000269|PubMed:16478479};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:10841550, ECO:0000269|PubMed:16478479};
CC Note=Divalent metal cations. Mg(2+), Ni(2+) and Mn(2+) are the most
CC effective. Co(2+) and Ca(2+) are only minimally effective.
CC {ECO:0000269|PubMed:10841550, ECO:0000269|PubMed:16478479};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=114 uM for CTP {ECO:0000269|PubMed:10841550};
CC KM=500 uM for MEP {ECO:0000269|PubMed:10841550};
CC Vmax=67 umol/min/mg enzyme {ECO:0000269|PubMed:10841550};
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC phosphate: step 2/6. {ECO:0000269|PubMed:10841550}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC {ECO:0000305|PubMed:18236010}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, stems and flowers, but not in
CC roots. {ECO:0000269|PubMed:12029484, ECO:0000269|PubMed:18236010}.
CC -!- INDUCTION: Circadian-regulated with a peak in the late period of the
CC light phase. {ECO:0000269|PubMed:15863698,
CC ECO:0000269|PubMed:18236010}.
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:18236010}.
CC -!- SIMILARITY: Belongs to the IspD/TarI cytidylyltransferase family. IspD
CC subfamily. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF230737; AAF61714.1; -; mRNA.
DR EMBL; AB037876; BAB21592.1; -; mRNA.
DR EMBL; AC004136; AAC18936.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC05588.1; -; Genomic_DNA.
DR EMBL; CP002685; ANM63324.1; -; Genomic_DNA.
DR EMBL; AK118110; BAC42737.1; -; mRNA.
DR EMBL; BT006120; AAP04105.1; -; mRNA.
DR PIR; T00613; T00613.
DR RefSeq; NP_001325418.1; NM_001335124.1.
DR RefSeq; NP_565286.1; NM_126305.3.
DR PDB; 1W77; X-ray; 2.00 A; A=76-302.
DR PDB; 2YC3; X-ray; 1.40 A; A=76-302.
DR PDB; 2YC5; X-ray; 1.60 A; A=76-302.
DR PDB; 2YCM; X-ray; 1.80 A; A=76-302.
DR PDB; 4NAI; X-ray; 1.50 A; A=76-302.
DR PDB; 4NAK; X-ray; 1.80 A; A=76-302.
DR PDB; 4NAL; X-ray; 1.80 A; A=76-302.
DR PDB; 4NAN; X-ray; 1.80 A; A=76-302.
DR PDB; 5MRM; X-ray; 1.80 A; A=76-302.
DR PDB; 5MRN; X-ray; 2.00 A; A=76-302.
DR PDB; 5MRO; X-ray; 1.80 A; A=76-302.
DR PDB; 5MRP; X-ray; 1.90 A; A=76-302.
DR PDB; 5MRQ; X-ray; 2.20 A; A=76-302.
DR PDBsum; 1W77; -.
DR PDBsum; 2YC3; -.
DR PDBsum; 2YC5; -.
DR PDBsum; 2YCM; -.
DR PDBsum; 4NAI; -.
DR PDBsum; 4NAK; -.
DR PDBsum; 4NAL; -.
DR PDBsum; 4NAN; -.
DR PDBsum; 5MRM; -.
DR PDBsum; 5MRN; -.
DR PDBsum; 5MRO; -.
DR PDBsum; 5MRP; -.
DR PDBsum; 5MRQ; -.
DR AlphaFoldDB; P69834; -.
DR SMR; P69834; -.
DR STRING; 3702.AT2G02500.1; -.
DR BindingDB; P69834; -.
DR ChEMBL; CHEMBL2285353; -.
DR iPTMnet; P69834; -.
DR PaxDb; P69834; -.
DR PRIDE; P69834; -.
DR ProteomicsDB; 250652; -.
DR EnsemblPlants; AT2G02500.1; AT2G02500.1; AT2G02500.
DR EnsemblPlants; AT2G02500.2; AT2G02500.2; AT2G02500.
DR GeneID; 814779; -.
DR Gramene; AT2G02500.1; AT2G02500.1; AT2G02500.
DR Gramene; AT2G02500.2; AT2G02500.2; AT2G02500.
DR KEGG; ath:AT2G02500; -.
DR Araport; AT2G02500; -.
DR TAIR; locus:2065264; AT2G02500.
DR eggNOG; ENOG502QUUE; Eukaryota.
DR HOGENOM; CLU_061281_0_0_1; -.
DR InParanoid; P69834; -.
DR OMA; ERQHSVY; -.
DR OrthoDB; 1356473at2759; -.
DR PhylomeDB; P69834; -.
DR BioCyc; ARA:AT2G02500-MON; -.
DR BioCyc; MetaCyc:AT2G02500-MON; -.
DR BRENDA; 2.7.7.60; 399.
DR SABIO-RK; P69834; -.
DR UniPathway; UPA00056; UER00093.
DR EvolutionaryTrace; P69834; -.
DR PRO; PR:P69834; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; P69834; baseline and differential.
DR Genevisible; P69834; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0050518; F:2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity; IDA:TAIR.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; TAS:TAIR.
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 1: Evidence at protein level;
KW 3D-structure; Acetylation; Chloroplast; Isoprene biosynthesis;
KW Nucleotidyltransferase; Plastid; Reference proteome; Transferase;
KW Transit peptide.
FT TRANSIT 1..61
FT /note="Chloroplast"
FT /evidence="ECO:0000255, ECO:0007744|PubMed:22223895"
FT CHAIN 62..302
FT /note="2-C-methyl-D-erythritol 4-phosphate
FT cytidylyltransferase, chloroplastic"
FT /id="PRO_0000016478"
FT SITE 91
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT SITE 98
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT SITE 228
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000250"
FT SITE 284
FT /note="Positions MEP for the nucleophilic attack"
FT /evidence="ECO:0000250"
FT MOD_RES 62
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT STRAND 79..84
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 98..100
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 108..118
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 122..128
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 131..133
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 134..138
FT /evidence="ECO:0007829|PDB:2YC3"
FT TURN 139..143
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 144..151
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 157..165
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 173..179
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 187..200
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 201..208
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:4NAI"
FT STRAND 222..225
FT /evidence="ECO:0007829|PDB:4NAI"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:4NAI"
FT STRAND 232..240
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 242..255
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:4NAI"
FT HELIX 264..268
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 269..271
FT /evidence="ECO:0007829|PDB:2YC3"
FT STRAND 274..277
FT /evidence="ECO:0007829|PDB:2YC3"
FT HELIX 288..298
FT /evidence="ECO:0007829|PDB:2YC3"
SQ SEQUENCE 302 AA; 33937 MW; 7881DC5C8CE37B06 CRC64;
MAMLQTNLGF ITSPTFLCPK LKVKLNSYLW FSYRSQVQKL DFSKRVNRSY KRDALLLSIK
CSSSTGFDNS NVVVKEKSVS VILLAGGQGK RMKMSMPKQY IPLLGQPIAL YSFFTFSRMP
EVKEIVVVCD PFFRDIFEEY EESIDVDLRF AIPGKERQDS VYSGLQEIDV NSELVCIHDS
ARPLVNTEDV EKVLKDGSAV GAAVLGVPAK ATIKEVNSDS LVVKTLDRKT LWEMQTPQVI
KPELLKKGFE LVKSEGLEVT DDVSIVEYLK HPVYVSQGSY TNIKVTTPDD LLLAERILSE
DS
