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Protein

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

Gene

ispD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).

Miscellaneous

There are no coordination bonds that occur between IspD and magnesium in any of the complexes examined to date.

Catalytic activityi

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

Cofactori

pH dependencei

Optimum pH is 8.3.

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 (dxr)
  2. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (ispD)
  3. 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (ispE)
  4. 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispF)
  5. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) (ispG)
  6. 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (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
Sitei20Transition state stabilizer1 Publication1
Sitei27Transition state stabilizer1 Publication1
Sitei157Positions MEP for the nucleophilic attack1 Publication1
Sitei213Positions MEP for the nucleophilic attack1 Publication1

GO - Molecular functioni

  • 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity Source: EcoCyc
  • identical protein binding Source: EcoCyc
  • magnesium ion binding Source: EcoCyc

GO - Biological processi

Keywordsi

Molecular functionNucleotidyltransferase, Transferase
Biological processIsoprene biosynthesis
LigandCobalt, Magnesium, Manganese

Enzyme and pathway databases

BioCyciEcoCyc:G7423-MONOMER
MetaCyc:G7423-MONOMER
BRENDAi2.7.7.60 2026
SABIO-RKiQ46893
UniPathwayiUPA00056; UER00093

Names & Taxonomyi

Protein namesi
Recommended name:
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC:2.7.7.60)
Alternative name(s):
4-diphosphocytidyl-2C-methyl-D-erythritol synthase
CDP-ME synthase
MEP cytidylyltransferase
Short name:
MCT
Gene namesi
Name:ispD
Synonyms:ygbP
Ordered Locus Names:b2747, JW2717
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13110 ispD

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi27K → A or S: Strong decrease in activity. 1 Publication1
Mutagenesisi140T → I: Loss of activity. 1 Publication1
Mutagenesisi191E → K: Loss of activity. 1 Publication1
Mutagenesisi213K → S: Decrease in activity. 1 Publication1

Chemistry databases

DrugBankiDB03687 4-Diphosphocytidyl-2-C-Methyl-D-Erythritol
DB02431 Cytidine-5'-Triphosphate

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00000755722 – 2362-C-methyl-D-erythritol 4-phosphate cytidylyltransferaseAdd BLAST235

Proteomic databases

PaxDbiQ46893
PRIDEiQ46893

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4262280, 173 interactors
IntActiQ46893, 2 interactors
STRINGi316385.ECDH10B_2915

Structurei

Secondary structure

1236
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 14Combined sources7
Helixi19 – 21Combined sources3
Beta strandi23 – 25Combined sources3
Helixi27 – 29Combined sources3
Beta strandi30 – 32Combined sources3
Helixi37 – 46Combined sources10
Beta strandi51 – 58Combined sources8
Helixi65 – 67Combined sources3
Helixi69 – 72Combined sources4
Beta strandi76 – 80Combined sources5
Helixi85 – 94Combined sources10
Beta strandi100 – 104Combined sources5
Helixi114 – 121Combined sources8
Helixi122 – 125Combined sources4
Beta strandi131 – 136Combined sources6
Beta strandi141 – 144Combined sources4
Beta strandi148 – 155Combined sources8
Beta strandi161 – 170Combined sources10
Helixi171 – 183Combined sources13
Helixi191 – 197Combined sources7
Beta strandi203 – 206Combined sources4
Helixi219 – 227Combined sources9
Helixi229 – 233Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1H3MX-ray2.40A/B2-236[»]
1I52X-ray1.50A1-236[»]
1INIX-ray1.82A1-236[»]
1INJX-ray1.55A1-236[»]
1VGTX-ray1.80A/B2-236[»]
1VGUX-ray2.80A/B2-236[»]
3N9WX-ray1.90A/B2-236[»]
ProteinModelPortaliQ46893
SMRiQ46893
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46893

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CE5 Bacteria
COG1211 LUCA
HOGENOMiHOG000218564
InParanoidiQ46893
KOiK00991
OMAiERQHSVY
PhylomeDBiQ46893

Family and domain databases

CDDicd02516 CDP-ME_synthetase, 1 hit
Gene3Di3.90.550.10, 1 hit
HAMAPiMF_00108 IspD, 1 hit
InterProiView protein in InterPro
IPR001228 IspD
IPR034683 IspD/TarI
IPR018294 ISPD_synthase_CS
IPR029044 Nucleotide-diphossugar_trans
PfamiView protein in Pfam
PF01128 IspD, 1 hit
SUPFAMiSSF53448 SSF53448, 1 hit
TIGRFAMsiTIGR00453 ispD, 1 hit
PROSITEiView protein in PROSITE
PS01295 ISPD, 1 hit

Sequencei

Sequence statusi: Complete.

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

Q46893-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATTHLDVCA VVPAAGFGRR MQTECPKQYL SIGNQTILEH SVHALLAHPR
60 70 80 90 100
VKRVVIAISP GDSRFAQLPL ANHPQITVVD GGDERADSVL AGLKAAGDAQ
110 120 130 140 150
WVLVHDAARP CLHQDDLARL LALSETSRTG GILAAPVRDT MKRAEPGKNA
160 170 180 190 200
IAHTVDRNGL WHALTPQFFP RELLHDCLTR ALNEGATITD EASALEYCGF
210 220 230
HPQLVEGRAD NIKVTRPEDL ALAEFYLTRT IHQENT
Length:236
Mass (Da):25,737
Last modified:January 23, 2007 - v3
Checksum:i6AD26690AC2CF201
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF230736 Genomic DNA Translation: AAF43207.1
AB037143 Genomic DNA Translation: BAA90761.1
U29579 Genomic DNA Translation: AAA69257.1
U00096 Genomic DNA Translation: AAC75789.1
AP009048 Genomic DNA Translation: BAE76824.1
PIRiG65055
RefSeqiNP_417227.1, NC_000913.3
WP_000246138.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75789; AAC75789; b2747
BAE76824; BAE76824; BAE76824
GeneIDi948269
KEGGiecj:JW2717
eco:b2747
PATRICifig|1411691.4.peg.3993

Similar proteinsi

Entry informationi

Entry nameiISPD_ECOLI
AccessioniPrimary (citable) accession number: Q46893
Secondary accession number(s): Q2MA82
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 155 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health