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Protein

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic

Gene

ISPD

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). Is essential for chloroplast development and required for pigments and gibberellins biosynthesis.3 Publications

Catalytic activityi

CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.

Cofactori

Mg2+2 Publications, Ni2+2 Publications, Mn2+2 PublicationsNote: Divalent metal cations. Mg2+, Ni2+ and Mn2+ are the most effective. Co2+ and Ca2+ are only minimally effective.2 Publications

Kineticsi

  1. KM=114 µM for CTP1 Publication
  2. KM=500 µM for MEP1 Publication
  1. Vmax=67 µmol/min/mg enzyme1 Publication

Pathwayi: isopentenyl diphosphate biosynthesis via DXP pathway

This protein is involved in step 2 of the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate.
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. 1-deoxy-D-xylulose 5-phosphate reductoisomerase, chloroplastic (DXR)
  2. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic (ISPD)
  3. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, chloroplastic (ISPE)
  4. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic (ISPF)
  5. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin), chloroplastic (ISPG)
  6. 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic (ISPH)
This subpathway is part of the pathway isopentenyl diphosphate biosynthesis via DXP pathway, which is itself part of Isoprenoid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate, the pathway isopentenyl diphosphate biosynthesis via DXP pathway and in Isoprenoid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei91 – 911Transition state stabilizerBy similarity
Sitei98 – 981Transition state stabilizerBy similarity
Sitei228 – 2281Positions MEP for the nucleophilic attackBy similarity
Sitei284 – 2841Positions MEP for the nucleophilic attackBy similarity

GO - Molecular functioni

  • 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity Source: TAIR

GO - Biological processi

  • isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Isoprene biosynthesis

Enzyme and pathway databases

BioCyciARA:AT2G02500-MONOMER.
MetaCyc:AT2G02500-MONOMER.
BRENDAi2.7.7.60. 399.
UniPathwayiUPA00056; UER00093.

Names & Taxonomyi

Protein namesi
Recommended name:
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic (EC:2.7.7.60)
Alternative name(s):
4-diphosphocytidyl-2C-methyl-D-erythritol synthase
MEP cytidylyltransferase
Short name:
AtMECT
Short name:
AtMEPCT
Gene namesi
Name:ISPD
Synonyms:MCT, MECT, MEPCT
Ordered Locus Names:At2g02500
ORF Names:T8K22.20
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

TAIRiAT2G02500.

Subcellular locationi

  • Plastidchloroplast stroma 1 Publication

GO - Cellular componenti

  • chloroplast Source: TAIR
  • chloroplast stroma Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Plastid

Pathology & Biotechi

Disruption phenotypei

Albino phenotype and seedling lethal when homozygous. The phenotype is caused by an early arrest in chloroplast differentiation.1 Publication

Chemistry

ChEMBLiCHEMBL2285353.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 6161ChloroplastSequence analysisCombined sourcesAdd
BLAST
Chaini62 – 3022412-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplasticPRO_0000016478Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei62 – 621N-acetylserineCombined sources

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP69834.
PRIDEiP69834.

Expressioni

Tissue specificityi

Expressed in leaves, stems and flowers, but not in roots.2 Publications

Inductioni

Circadian-regulated with a peak in the late period of the light phase.2 Publications

Gene expression databases

GenevisibleiP69834. AT.

Interactioni

Protein-protein interaction databases

STRINGi3702.AT2G02500.1.

Structurei

Secondary structure

1
302
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi79 – 846Combined sources
Helixi98 – 1003Combined sources
Beta strandi101 – 1033Combined sources
Helixi108 – 11811Combined sources
Beta strandi122 – 1287Combined sources
Helixi131 – 1333Combined sources
Helixi134 – 1385Combined sources
Turni139 – 1435Combined sources
Beta strandi144 – 1518Combined sources
Helixi157 – 1659Combined sources
Beta strandi173 – 1797Combined sources
Helixi187 – 20014Combined sources
Beta strandi201 – 2088Combined sources
Beta strandi214 – 2163Combined sources
Beta strandi222 – 2254Combined sources
Helixi228 – 2303Combined sources
Beta strandi232 – 2409Combined sources
Helixi242 – 25514Combined sources
Beta strandi260 – 2623Combined sources
Helixi264 – 2685Combined sources
Beta strandi269 – 2713Combined sources
Beta strandi274 – 2774Combined sources
Helixi288 – 29811Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W77X-ray2.00A76-302[»]
2YC3X-ray1.40A76-302[»]
2YC5X-ray1.60A76-302[»]
2YCMX-ray1.80A76-302[»]
4NAIX-ray1.50A76-302[»]
4NAKX-ray1.80A76-302[»]
4NALX-ray1.80A76-302[»]
4NANX-ray1.80A76-302[»]
ProteinModelPortaliP69834.
SMRiP69834. Positions 76-300.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69834.

Family & Domainsi

Sequence similaritiesi

Belongs to the IspD family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IIH2. Eukaryota.
COG1211. LUCA.
HOGENOMiHOG000218563.
InParanoidiP69834.
KOiK00991.
OMAiQAYTPQM.
PhylomeDBiP69834.

Family and domain databases

Gene3Di3.90.550.10. 1 hit.
HAMAPiMF_00108. IspD.
InterProiIPR001228. IspD.
IPR018294. ISPD_synthase_CS.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PfamiPF01128. IspD. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
TIGRFAMsiTIGR00453. ispD. 1 hit.
PROSITEiPS01295. ISPD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P69834-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAMLQTNLGF ITSPTFLCPK LKVKLNSYLW FSYRSQVQKL DFSKRVNRSY
60 70 80 90 100
KRDALLLSIK CSSSTGFDNS NVVVKEKSVS VILLAGGQGK RMKMSMPKQY
110 120 130 140 150
IPLLGQPIAL YSFFTFSRMP EVKEIVVVCD PFFRDIFEEY EESIDVDLRF
160 170 180 190 200
AIPGKERQDS VYSGLQEIDV NSELVCIHDS ARPLVNTEDV EKVLKDGSAV
210 220 230 240 250
GAAVLGVPAK ATIKEVNSDS LVVKTLDRKT LWEMQTPQVI KPELLKKGFE
260 270 280 290 300
LVKSEGLEVT DDVSIVEYLK HPVYVSQGSY TNIKVTTPDD LLLAERILSE

DS
Length:302
Mass (Da):33,937
Last modified:May 24, 2005 - v1
Checksum:i7881DC5C8CE37B06
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF230737 mRNA. Translation: AAF61714.1.
AB037876 mRNA. Translation: BAB21592.1.
AC004136 Genomic DNA. Translation: AAC18936.2.
CP002685 Genomic DNA. Translation: AEC05588.1.
AK118110 mRNA. Translation: BAC42737.1.
BT006120 mRNA. Translation: AAP04105.1.
PIRiT00613.
RefSeqiNP_565286.1. NM_126305.2.
UniGeneiAt.10212.

Genome annotation databases

EnsemblPlantsiAT2G02500.1; AT2G02500.1; AT2G02500.
GeneIDi814779.
GrameneiAT2G02500.1; AT2G02500.1; AT2G02500.
KEGGiath:AT2G02500.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF230737 mRNA. Translation: AAF61714.1.
AB037876 mRNA. Translation: BAB21592.1.
AC004136 Genomic DNA. Translation: AAC18936.2.
CP002685 Genomic DNA. Translation: AEC05588.1.
AK118110 mRNA. Translation: BAC42737.1.
BT006120 mRNA. Translation: AAP04105.1.
PIRiT00613.
RefSeqiNP_565286.1. NM_126305.2.
UniGeneiAt.10212.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W77X-ray2.00A76-302[»]
2YC3X-ray1.40A76-302[»]
2YC5X-ray1.60A76-302[»]
2YCMX-ray1.80A76-302[»]
4NAIX-ray1.50A76-302[»]
4NAKX-ray1.80A76-302[»]
4NALX-ray1.80A76-302[»]
4NANX-ray1.80A76-302[»]
ProteinModelPortaliP69834.
SMRiP69834. Positions 76-300.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT2G02500.1.

Chemistry

ChEMBLiCHEMBL2285353.

Proteomic databases

PaxDbiP69834.
PRIDEiP69834.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT2G02500.1; AT2G02500.1; AT2G02500.
GeneIDi814779.
GrameneiAT2G02500.1; AT2G02500.1; AT2G02500.
KEGGiath:AT2G02500.

Organism-specific databases

TAIRiAT2G02500.

Phylogenomic databases

eggNOGiENOG410IIH2. Eukaryota.
COG1211. LUCA.
HOGENOMiHOG000218563.
InParanoidiP69834.
KOiK00991.
OMAiQAYTPQM.
PhylomeDBiP69834.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00093.
BioCyciARA:AT2G02500-MONOMER.
MetaCyc:AT2G02500-MONOMER.
BRENDAi2.7.7.60. 399.

Miscellaneous databases

EvolutionaryTraceiP69834.
PROiP69834.

Gene expression databases

GenevisibleiP69834. AT.

Family and domain databases

Gene3Di3.90.550.10. 1 hit.
HAMAPiMF_00108. IspD.
InterProiIPR001228. IspD.
IPR018294. ISPD_synthase_CS.
IPR029044. Nucleotide-diphossugar_trans.
[Graphical view]
PfamiPF01128. IspD. 1 hit.
[Graphical view]
SUPFAMiSSF53448. SSF53448. 1 hit.
TIGRFAMsiTIGR00453. ispD. 1 hit.
PROSITEiPS01295. ISPD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Biosynthesis of terpenoids: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase of Arabidopsis thaliana."
    Rohdich F., Wungsintaweekul J., Eisenreich W., Richter G., Schuhr C.A., Hecht S., Zenk M.H., Bacher A.
    Proc. Natl. Acad. Sci. U.S.A. 97:6451-6456(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
    Strain: cv. Columbia.
  2. "Antisense and chemical suppression of the nonmevalonate pathway affects ent-kaurene biosynthesis in Arabidopsis."
    Okada K., Kawaide H., Kuzuyama T., Seto H., Curtis I.S., Kamiya Y.
    Planta 215:339-344(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  7. "The Arabidopsis IspH homolog is involved in the plastid nonmevalonate pathway of isoprenoid biosynthesis."
    Hsieh M.H., Goodman H.M.
    Plant Physiol. 138:641-653(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  8. "Chloroplast localization of methylerythritol 4-phosphate pathway enzymes and regulation of mitochondrial genes in ispD and ispE albino mutants in Arabidopsis."
    Hsieh M.H., Chang C.Y., Hsu S.J., Chen J.J.
    Plant Mol. Biol. 66:663-673(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION, DISRUPTION PHENOTYPE.
  9. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-62, CLEAVAGE OF TRANSIT PEPTIDE [LARGE SCALE ANALYSIS] AFTER CYS-61, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. "The crystal structure of a plant 2C-methyl-D-erythritol 4-phosphate cytidylyltransferase exhibits a distinct quaternary structure compared to bacterial homologues and a possible role in feedback regulation for cytidine monophosphate."
    Gabrielsen M., Kaiser J., Rohdich F., Eisenreich W., Laupitz R., Bacher A., Bond C.S., Hunter W.N.
    FEBS J. 273:1065-1073(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 76-302, COFACTOR.

Entry informationi

Entry nameiISPD_ARATH
AccessioniPrimary (citable) accession number: P69834
Secondary accession number(s): O64726, Q9LL91
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 24, 2005
Last sequence update: May 24, 2005
Last modified: February 17, 2016
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.