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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)DescriptionActionsGraphical viewLength
Sitei91Transition state stabilizerBy similarity1
Sitei98Transition state stabilizerBy similarity1
Sitei228Positions MEP for the nucleophilic attackBy similarity1
Sitei284Positions MEP for the nucleophilic attackBy similarity1

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 databases

ChEMBLiCHEMBL2285353.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 61ChloroplastSequence analysisCombined sourcesAdd BLAST61
ChainiPRO_000001647862 – 3022-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplasticAdd BLAST241

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei62N-acetylserineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP69834.

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

1302
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi79 – 84Combined sources6
Helixi98 – 100Combined sources3
Beta strandi101 – 103Combined sources3
Helixi108 – 118Combined sources11
Beta strandi122 – 128Combined sources7
Helixi131 – 133Combined sources3
Helixi134 – 138Combined sources5
Turni139 – 143Combined sources5
Beta strandi144 – 151Combined sources8
Helixi157 – 165Combined sources9
Beta strandi173 – 179Combined sources7
Helixi187 – 200Combined sources14
Beta strandi201 – 208Combined sources8
Beta strandi214 – 216Combined sources3
Beta strandi222 – 225Combined sources4
Helixi228 – 230Combined sources3
Beta strandi232 – 240Combined sources9
Helixi242 – 255Combined sources14
Beta strandi260 – 262Combined sources3
Helixi264 – 268Combined sources5
Beta strandi269 – 271Combined sources3
Beta strandi274 – 277Combined sources4
Helixi288 – 298Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP69834.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiENOG410IIH2. Eukaryota.
COG1211. LUCA.
HOGENOMiHOG000218563.
InParanoidiP69834.
KOiK00991.
OMAiQAYTPQM.
OrthoDBiEOG09360I4J.
PhylomeDBiP69834.

Family and domain databases

CDDicd02516. CDP-ME_synthetase. 1 hit.
Gene3Di3.90.550.10. 1 hit.
HAMAPiMF_00108. IspD. 1 hit.
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_126305.3.
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_126305.3.
UniGeneiAt.10212.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT2G02500.1.

Chemistry databases

ChEMBLiCHEMBL2285353.

Proteomic databases

PaxDbiP69834.

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.
OrthoDBiEOG09360I4J.
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

CDDicd02516. CDP-ME_synthetase. 1 hit.
Gene3Di3.90.550.10. 1 hit.
HAMAPiMF_00108. IspD. 1 hit.
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...

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: November 30, 2016
This is version 99 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.