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

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Reviewed, UniProtKB/Swiss-Prot Q46893 (ISPD_ECOLI)

Last modified November 3, 2009. Version 91. History...

Clusters with 100%, 90%, 50% identity |

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

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
    MEP cytidylyltransferase
      Short name=MCT
    CDP-ME synthetase

Gene names

Name:	ispD
Synonyms:	ygbP
Ordered Locus Names:	b2747, JW2717

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	236 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). HAMAP MF_00108
Catalytic activity	CTP + 2-C-methyl-D-erythritol 4-phosphate = diphosphate + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. HAMAP MF_00108
Cofactor	Magnesium, manganese or cobalt. HAMAP MF_00108
Pathway	Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 2/6. HAMAP MF_00108
Subunit structure	Homodimer. HAMAP MF_00108
Miscellaneous	There are no coordination bonds that occur between ispD and magnesium in any of the complexes examined to date. HAMAP MF_00108
Sequence similarities	Belongs to the ispD family.
Biophysicochemical properties	pH dependence: Optimum pH is 8.3. HAMAP MF_00108

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Ontologies

Keywords
Biological process	Isoprene biosynthesis
Ligand	Cobalt Magnesium Manganese
Molecular function	Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	terpenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP
Molecular function	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity Inferred from electronic annotation. Source: HAMAP cobalt ion binding Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW manganese ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed HAMAP MF_00108

Chain

2 – 236

235

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase HAMAP MF_00108

PRO_0000075572

Sites

Site

Transition state stabilizer HAMAP MF_00108

Site

Transition state stabilizer HAMAP MF_00108

Site

157

Positions MEP for the nucleophilic attack HAMAP MF_00108

Site

213

Positions MEP for the nucleophilic attack HAMAP MF_00108

Experimental info

Mutagenesis

K → A or S: Strong decrease in activity. Ref.7

Mutagenesis

140

T → I: Loss of activity. Ref.5

Mutagenesis

191

E → K: Loss of activity. Ref.5

Mutagenesis

213

K → S: Decrease in activity. Ref.7

Secondary structure

236

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

Q46893-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 6AD26690AC2CF201
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FASTA

236

25,737

        10         20         30         40         50         60 
MATTHLDVCA VVPAAGFGRR MQTECPKQYL SIGNQTILEH SVHALLAHPR VKRVVIAISP 

        70         80         90        100        110        120 
GDSRFAQLPL ANHPQITVVD GGDERADSVL AGLKAAGDAQ WVLVHDAARP CLHQDDLARL 

       130        140        150        160        170        180 
LALSETSRTG GILAAPVRDT MKRAEPGKNA IAHTVDRNGL WHALTPQFFP RELLHDCLTR 

       190        200        210        220        230 
ALNEGATITD EASALEYCGF HPQLVEGRAD NIKVTRPEDL ALAEFYLTRT IHQENT

« Hide

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 10518523] [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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] 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: 16738553] [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: 12859972] [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: 11468415] [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: 11427897] [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: 12595740] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
+	Additional computationally mapped references.

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Cross-references

Sequence databases

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.

PIR

G65055.

RefSeq

AP_003314.1.
NP_417227.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H3M	X-ray	2.40	A/B	2-236	[»]
1I52	X-ray	1.50	A	1-236	[»]
1INI	X-ray	1.82	A	1-236	[»]
1INJ	X-ray	1.55	A	1-236	[»]
1VGT	X-ray	1.80	A/B	2-235	[»]
1VGU	X-ray	2.80	A/B	2-235	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q46893.

Genome annotation databases

GeneID

948269.

GenomeReviews

Gene locus JW2717 in contig AP009048_GR.
Gene locus b2747 in contig U00096_GR.

KEGG

ecj:JW2717.
eco:b2747.

Organism-specific databases

EchoBASE

EB2913.

EcoGene

EG13110. ispD.

CMR

Search...

Phylogenomic databases

HOGENOM

Q46893.

OMA

DDPYWPG.

Enzyme and pathway databases

BioCyc

EcoCyc:G7423-MON.
MetaCyc:G7423-MON.

Gene expression databases

Genevestigator

Q46893.

Family and domain databases

HAMAP

MF_00108.
[Tree]

InterPro

IPR001228. ISPD_synthase.
IPR018294. ISPD_synthase_CS.
[Graphical view]

Pfam

PF01128. IspD. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00453. ispD. 1 hit.

PROSITE

PS01295. ISPD. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

ISPD_ECOLI

Accession

Primary (citable) accession number: Q46893
Secondary accession number(s): Q2MA82

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 91 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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