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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)LengthDescriptionGraphical viewFeature identifierActions
Sitei20 – 201Transition state stabilizer
Sitei27 – 271Transition state stabilizer
Sitei157 – 1571Positions MEP for the nucleophilic attack
Sitei213 – 2131Positions MEP for the nucleophilic attack

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi27 – 271K → A or S: Strong decrease in activity. 1 Publication
Mutagenesisi140 – 1401T → I: Loss of activity. 1 Publication
Mutagenesisi191 – 1911E → K: Loss of activity. 1 Publication
Mutagenesisi213 – 2131K → S: Decrease in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved
Chaini2 – 2362352-C-methyl-D-erythritol 4-phosphate cytidylyltransferasePRO_0000075572Add
BLAST

Proteomic databases

PaxDbiQ46893.

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4262280. 173 interactions.
IntActiQ46893. 2 interactions.
STRINGi511145.b2747.

Structurei

Secondary structure

1
236
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 147Combined sources
Helixi19 – 213Combined sources
Beta strandi23 – 253Combined sources
Helixi27 – 293Combined sources
Beta strandi30 – 323Combined sources
Helixi37 – 4610Combined sources
Beta strandi51 – 588Combined sources
Helixi65 – 673Combined sources
Helixi69 – 724Combined sources
Beta strandi76 – 805Combined sources
Helixi85 – 9410Combined sources
Beta strandi100 – 1045Combined sources
Helixi114 – 1218Combined sources
Helixi122 – 1254Combined sources
Beta strandi131 – 1366Combined sources
Beta strandi141 – 1444Combined sources
Beta strandi148 – 1558Combined sources
Beta strandi161 – 17010Combined sources
Helixi171 – 18313Combined sources
Helixi191 – 1977Combined sources
Beta strandi203 – 2064Combined sources
Helixi219 – 2279Combined sources
Helixi229 – 2335Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 5-229.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ46893.

Family & Domainsi

Sequence similaritiesi

Belongs to the IspD family.Curated

Phylogenomic databases

eggNOGiENOG4105CE5. Bacteria.
COG1211. LUCA.
HOGENOMiHOG000218564.
InParanoidiQ46893.
KOiK00991.
OMAiQAYTPQM.
OrthoDBiEOG6J48RZ.
PhylomeDBiQ46893.

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.

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
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. Positions 5-229.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262280. 173 interactions.
IntActiQ46893. 2 interactions.
STRINGi511145.b2747.

Proteomic databases

PaxDbiQ46893.

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.
OrthoDBiEOG6J48RZ.
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

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. "Cytidine 5'-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methylerythritol."
    Rohdich F., Wungsintaweekul J., Fellermeier M., Sagner S., Herz S., Kis K., Eisenreich W., Bacher A., Zenk M.H.
    Proc. Natl. Acad. Sci. U.S.A. 96:11758-11763(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, CHARACTERIZATION.
    Strain: K12 / DH5-alpha.
  2. "Formation of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol from 2-C-methyl-D-erythritol 4-phosphate by 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, a new enzyme in the nonmevalonate pathway."
    Kuzuyama T., Takagi M., Kaneda K., Dairi T., Seto H.
    Tetrahedron Lett. 41:703-706(2000)
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Identification of lethal mutations in Escherichia coli genes encoding enzymes of the methylerythritol phosphate pathway."
    Sauret-Gueeto S., Ramos-Valdivia A., Ibanez E., Boronat A., Rodriguez-Concepcion M.
    Biochem. Biophys. Res. Commun. 307:408-415(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF THR-140 AND GLU-191.
  6. "Crystallization and preliminary X-ray diffraction studies of recombinant Escherichia coli 4-diphosphocytidyl-2-C-methyl-D-erythritol synthetase."
    Kemp L.E., Bond C.S., Hunter W.N.
    Acta Crystallogr. D 57:1189-1191(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION.
  7. "Structure of 4-diphosphocytidyl-2-C-methylerythritol synthetase involved in mevalonate-independent isoprenoid biosynthesis."
    Richard S.B., Bowman M.E., Kwiatkowski W., Kang I., Chow C., Lillo A.M., Cane D.E., Noel J.P.
    Nat. Struct. Biol. 8:641-648(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH CTP-MG(2+) AND IN COMPLEX WITH CDP-ME-MG(2+), MUTAGENESIS OF LYS-27 AND LYS-213.
    Strain: K12.
  8. "Structure of a tetragonal crystal form of Escherichia coli 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase."
    Kemp L.E., Bond C.S., Hunter W.N.
    Acta Crystallogr. D 59:607-610(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).

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: January 20, 2016
This is version 145 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.