P62615 (ISPE_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Short name=CMK
EC=2.7.1.148

Alternative name(s):
4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase

Gene names

Name:	ispE
Synonyms:	ipk, ychB
Ordered Locus Names:	b1208, JW1199

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	283 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol. Phosphorylates isopentenyl phosphate at low rates. Also acts on isopentenol, and, much less efficiently, dimethylallyl alcohol. Dimethylallyl monophosphate does not serve as a substrate. HAMAP-Rule MF_00061
Catalytic activity	ATP + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = ADP + 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. HAMAP-Rule MF_00061
Pathway	Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate: step 3/6. HAMAP-Rule MF_00061
Subunit structure	Homodimer By similarity.
Sequence similarities	Belongs to the GHMP kinase family. IspE subfamily.
Caution	Was originally (Ref.1) thought to be an isopentenyl monophosphate kinase.
Sequence caution	The sequence BAA01106.1 differs from that shown. Reason: Frameshift at position 50.

Ontologies

Keywords
Biological process	Isoprene biosynthesis
Ligand	ATP-binding Nucleotide-binding
Molecular function	Kinase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway Inferred from electronic annotation. Source: UniProtKB-UniPathway terpenoid biosynthetic process Inferred from electronic annotation. Source: HAMAP ubiquinone biosynthetic process Inferred from direct assay Ref.5. Source: EcoCyc
Molecular_function	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity Inferred from direct assay Ref.5. Source: EcoCyc ATP binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
glmS	P17169	1	EBI-562202,EBI-551022

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 283

283

4-diphosphocytidyl-2-C-methyl-D-erythritol kinase HAMAP-Rule MF_00061

PRO_0000189215

Regions

Nucleotide binding

99 – 109

11

ATP Potential

Sites

Active site

10

1

By similarity

Active site

141

1

By similarity

Experimental info

Mutagenesis

239

1

G → R: Loss of activity. Ref.10

Mutagenesis

240

1

T → I: Loss of activity. Ref.10

Sequence conflict

208 – 276

69

SNDCE…GANLS → TQAYGRANTKGAPFRRTAVK CRSLGKLLLECAGKCLLRVE AVLQRDVQNRTRSQA in BAA01106. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

283

Helix Strand Turn

Details...

Beta strand

2 – 20

19

Beta strand

26 – 49

24

Beta strand

51 – 53

3

Helix

62 – 64

3

Helix

66 – 80

15

Beta strand

89 – 95

7

Helix

106 – 121

16

Helix

128 – 136

9

Helix

142 – 147

6

Beta strand

151 – 154

4

Turn

155 – 158

4

Beta strand

159 – 162

4

Beta strand

169 – 173

5

Helix

181 – 185

5

Helix

199 – 203

5

Helix

212 – 218

7

Helix

220 – 230

11

Beta strand

235 – 237

3

Beta strand

244 – 250

7

Helix

251 – 260

10

Beta strand

267 – 275

9

Helix

277 – 281

5

Sequences

	Sequence		Length	Mass (Da)
	P62615 [UniParc]. Last modified July 19, 2004. Version 1. Checksum: 59A2921FA05D13E1	FASTA	283	30,925
	10 20 30 40 50 60 MRTQWPSPAK LNLFLYITGQ RADGYHTLQT LFQFLDYGDT ISIELRDDGD IRLLTPVEGV 70 80 90 100 110 120 EHEDNLIVRA ARLLMKTAAD SGRLPTGSGA NISIDKRLPM GGGLGGGSSN AATVLVALNH 130 140 150 160 170 180 LWQCGLSMDE LAEMGLTLGA DVPVFVRGHA AFAEGVGEIL TPVDPPEKWY LVAHPGVSIP 190 200 210 220 230 240 TPVIFKDPEL PRNTPKRSIE TLLKCEFSND CEVIARKRFR EVDAVLSWLL EYAPSRLTGT 250 260 270 280 GACVFAEFDT ESEARQVLEQ APEWLNGFVA KGANLSPLHR AML

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of genes involved in the biosynthesis of delta-aminolevulinic acid in Escherichia coli." Ikemi M., Murakami K., Hashimoto M., Murooka Y. Gene 121:127-132(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Characterization of the hemA-prs region of the Escherichia coli and Salmonella typhimurium chromosomes: identification of two open reading frames and implications for prs expression." Post D.A., Hove-Jensen B., Switzer R.L. J. Gen. Microbiol. 139:259-266(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Expression of genes kdsA and kdsB involved in 3-deoxy-D-manno-octulosonic acid metabolism and biosynthesis of enterobacterial lipopolysaccharide is growth phase regulated primarily at the transcriptional level in Escherichia coli K-12." Strohmaier H., Remler P., Renner W., Hoegenauer G. J. Bacteriol. 177:4488-4500(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[4]	"Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: isopentenyl monophosphate kinase catalyzes the terminal enzymatic step." Lange B.M., Croteau R. Proc. Natl. Acad. Sci. U.S.A. 96:13714-13719(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Biosynthesis of terpenoids: YchB protein of Escherichia coli phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol." Luettgen H., Rohdich F., Herz S., Wungsintaweekul J., Hecht S., Schuhr C.A., Fellermeier M., Sagner S., Zenk M.H., Bacher A., Eisenreich W. Proc. Natl. Acad. Sci. U.S.A. 97:1062-1067(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
[6]	"Studies on the nonmevalonate pathway: conversion of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol to its 2-phospho derivative by 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase." Kuzuyama T., Takagi M., Kaneda K., Watanabe H., Dairi T., Seto H. Tetrahedron Lett. 41:2925-2928(2000) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[8]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[9]	"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.
[10]	"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 GLY-239 AND THR-240.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D10264 Genomic DNA. Translation: BAA01106.1. Frameshift.
M77237 Genomic DNA. Translation: AAA24434.1.
U18555 Genomic DNA. Translation: AAC43434.1.
AJ249325 Genomic DNA. Translation: CAB64963.1.
AF179284 Genomic DNA. Translation: AAF13867.1.
AF216300 Genomic DNA. Translation: AAF29530.1.
AB037116 Genomic DNA. Translation: BAA94247.1.
U00096 Genomic DNA. Translation: AAC74292.1.
AP009048 Genomic DNA. Translation: BAA36066.1.

PIR

B47706.

RefSeq

NP_415726.1. NC_000913.2.
YP_489475.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2WW4	X-ray	2.00	A/B	1-283	[»]

ProteinModelPortal

P62615.

SMR

P62615. Positions 1-282.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48028N.

IntAct

P62615. 1 interaction.

STRING

511145.b1208.

Proteomic databases

PaxDb

P62615.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74292; AAC74292; b1208.
BAA36066; BAA36066; BAA36066.

GeneID

12931821.
945774.

KEGG

ecj:Y75_p1180.
eco:b1208.

PATRIC

32117668. VBIEscCol129921_1256.

Organism-specific databases

EchoBASE

EB1271.

EcoGene

EG11294. ispE.

Phylogenomic databases

eggNOG

COG1947.

HOGENOM

HOG000019601.

KO

K00919.

OMA

TGACVFG.

ProtClustDB

PRK00343.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11294-MONOMER.
ECOL316407:JW1199-MONOMER.
MetaCyc:EG11294-MONOMER.

UniPathway

UPA00056; UER00094.

Gene expression databases

Genevestigator

P62615.

Family and domain databases

Gene3D

3.30.230.10. 1 hit.

HAMAP

MF_00061. IspE.

InterPro

IPR013750. GHMP_kinase_C_dom.
IPR006204. GHMP_kinase_N_dom.
IPR004424. IspE.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
[Graphical view]

PANTHER

PTHR20861:SF2. PTHR20861:SF2. 1 hit.

Pfam

PF08544. GHMP_kinases_C. 1 hit.
PF00288. GHMP_kinases_N. 1 hit.
[Graphical view]

PIRSF

PIRSF010376. IspE. 1 hit.

SUPFAM

SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.

TIGRFAMs

TIGR00154. ispE. 1 hit.

ProtoNet

Search...

Entry information

Entry name

ISPE_ECOLI

Accession

Primary (citable) accession number: P62615
Secondary accession number(s): P24209

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2004
Last sequence update:	July 19, 2004
Last modified:	May 1, 2013
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program