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

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Q46893 (ISPD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 112. History...

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

Documents (5) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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
CDP-ME synthase
MEP cytidylyltransferase
Short name=MCT

Gene names

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

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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

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.
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.
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

Ontologies

Keywords
Biological process	Isoprene biosynthesis
Ligand	Cobalt Magnesium Manganese
Molecular function	Nucleotidyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	isoprenoid biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW ubiquinone biosynthetic process Inferred from direct assay Ref.1. Source: EcoCyc
Molecular function	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity Inferred from direct assay. Source: EcoCyc
Complete GO annotation...

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

Site

Transition state stabilizer

Site

157

Positions MEP for the nucleophilic attack

Site

213

Positions MEP for the nucleophilic attack

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...

Sequences

Sequence

Length

Mass (Da)

Tools

Q46893 [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

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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

NP_417227.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]
3N9W	X-ray	1.90	A/B	2-236	[»]

ProteinModelPortal

Q46893.

SMR

Q46893. Positions 5-229.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q46893. 2 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000002647; EBESCP00000002647; EBESCG00000002160.
EBESCT00000015791; EBESCP00000015082; EBESCG00000014851.

GeneID

948269.

GenomeReviews

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

KEGG

ecj:JW2717.
eco:b2747.

PATRIC

32120900. VBIEscCol129921_2842.

Organism-specific databases

EchoBASE

EB2913.

EcoGene

EG13110. ispD.

Phylogenomic databases

eggNOG

COG1211.

GeneTree

EBGT00050000011058.

HOGENOM

HBG672839.

OMA

PSNIKVT.

PhylomeDB

Q46893.

ProtClustDB

PRK00155.

Enzyme and pathway databases

BioCyc

EcoCyc:G7423-MONOMER.
MetaCyc:G7423-MONOMER.

Gene expression databases

Genevestigator

Q46893.

Family and domain databases

HAMAP

MF_00108. IspD.
[Tree]

InterPro

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

K00991.

Pfam

PF01128. IspD. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00453. IspD. 1 hit.

PROSITE

PS01295. ISPD. 1 hit.
[Graphical view]

ProtoNet

Search...

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:	January 25, 2012
This is version 112 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Uncharacterized protein families (UPF)

List of uncharacterized protein family (UPF) entries

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents