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Protein

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

Gene

ispD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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).

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
Sitei27Transition state stabilizer1
Sitei157Positions MEP for the nucleophilic attack1
Sitei213Positions MEP for the nucleophilic attack1

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

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

Cobalt, Magnesium, Manganese

Enzyme and pathway databases

BioCyciEcoCyc:G7423-MONOMER.
ECOL316407:JW2717-MONOMER.
MetaCyc:G7423-MONOMER.
BRENDAi2.7.7.60. 2026.
SABIO-RKQ46893.
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
Complete GO annotation...

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

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.
STRINGi511145.b2747.

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.
OMAiQAYTPQM.
PhylomeDBiQ46893.

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.

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.
PATRICi32120900. VBIEscCol129921_2842.

Cross-referencesi

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.

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...

Protein-protein interaction databases

BioGridi4262280. 173 interactors.
IntActiQ46893. 2 interactors.
STRINGi511145.b2747.

Proteomic databases

PaxDbiQ46893.
PRIDEiQ46893.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75789; AAC75789; b2747.
BAE76824; BAE76824; BAE76824.
GeneIDi948269.
KEGGiecj:JW2717.
eco:b2747.
PATRICi32120900. VBIEscCol129921_2842.

Organism-specific databases

EchoBASEiEB2913.
EcoGeneiEG13110. ispD.

Phylogenomic databases

eggNOGiENOG4105CE5. Bacteria.
COG1211. LUCA.
HOGENOMiHOG000218564.
InParanoidiQ46893.
KOiK00991.
OMAiQAYTPQM.
PhylomeDBiQ46893.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00093.
BioCyciEcoCyc:G7423-MONOMER.
ECOL316407:JW2717-MONOMER.
MetaCyc:G7423-MONOMER.
BRENDAi2.7.7.60. 2026.
SABIO-RKQ46893.

Miscellaneous databases

EvolutionaryTraceiQ46893.
PROiQ46893.

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_ECOLI
AccessioniPrimary (citable) accession number: Q46893
Secondary accession number(s): Q2MA82
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 148 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  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
  5. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.