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Protein

4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

Gene

ispE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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.

Caution

Was originally thought to be an isopentenyl monophosphate kinase.1 Publication

Catalytic activityi

ATP + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = ADP + 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol.

Pathwayi: isopentenyl diphosphate biosynthesis via DXP pathway

This protein is involved in step 3 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
Active sitei10By similarity1
Active sitei141By similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi99 – 109ATPSequence analysisAdd BLAST11

GO - Molecular functioni

  • 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity Source: EcoCyc
  • ATP binding Source: EcoCyc

GO - Biological processi

Keywordsi

Molecular functionKinase, Transferase
Biological processIsoprene biosynthesis
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11294-MONOMER
MetaCyc:EG11294-MONOMER
BRENDAi2.7.1.148 2026
UniPathwayiUPA00056; UER00094

Names & Taxonomyi

Protein namesi
Recommended name:
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (EC:2.7.1.148)
Short name:
CMK
Alternative name(s):
4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase
Gene namesi
Name:ispE
Synonyms:ipk, ychB
Ordered Locus Names:b1208, JW1199
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11294 ispE

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi239G → R: Loss of activity. 1 Publication1
Mutagenesisi240T → I: Loss of activity. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL2366480

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001892151 – 2834-diphosphocytidyl-2-C-methyl-D-erythritol kinaseAdd BLAST283

Proteomic databases

PaxDbiP62615
PRIDEiP62615

Interactioni

Subunit structurei

Homodimer.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
glmSP171692EBI-562202,EBI-551022

Protein-protein interaction databases

BioGridi4260815, 299 interactors
DIPiDIP-48028N
IntActiP62615, 1 interactor
STRINGi316385.ECDH10B_1261

Structurei

Secondary structure

1283
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 20Combined sources19
Beta strandi26 – 49Combined sources24
Beta strandi51 – 53Combined sources3
Helixi62 – 64Combined sources3
Helixi66 – 80Combined sources15
Beta strandi89 – 95Combined sources7
Helixi106 – 121Combined sources16
Helixi128 – 136Combined sources9
Helixi142 – 147Combined sources6
Beta strandi151 – 154Combined sources4
Turni155 – 158Combined sources4
Beta strandi159 – 162Combined sources4
Beta strandi169 – 173Combined sources5
Helixi181 – 185Combined sources5
Helixi199 – 203Combined sources5
Helixi212 – 218Combined sources7
Helixi220 – 230Combined sources11
Beta strandi235 – 237Combined sources3
Beta strandi244 – 250Combined sources7
Helixi251 – 260Combined sources10
Beta strandi267 – 275Combined sources9
Helixi277 – 281Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2WW4X-ray2.00A/B1-283[»]
ProteinModelPortaliP62615
SMRiP62615
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GHMP kinase family. IspE subfamily.Curated

Phylogenomic databases

eggNOGiENOG4105CTR Bacteria
COG1947 LUCA
HOGENOMiHOG000019601
InParanoidiP62615
KOiK00919
OMAiRWPSPAK
PhylomeDBiP62615

Family and domain databases

Gene3Di3.30.230.10, 1 hit
3.30.70.890, 1 hit
HAMAPiMF_00061 IspE, 1 hit
InterProiView protein in InterPro
IPR013750 GHMP_kinase_C_dom
IPR036554 GHMP_kinase_C_sf
IPR006204 GHMP_kinase_N_dom
IPR004424 IspE
IPR020568 Ribosomal_S5_D2-typ_fold
IPR014721 Ribosomal_S5_D2-typ_fold_subgr
PfamiView protein in Pfam
PF08544 GHMP_kinases_C, 1 hit
PF00288 GHMP_kinases_N, 1 hit
PIRSFiPIRSF010376 IspE, 1 hit
SUPFAMiSSF54211 SSF54211, 1 hit
SSF55060 SSF55060, 1 hit
TIGRFAMsiTIGR00154 ispE, 1 hit

Sequencei

Sequence statusi: Complete.

P62615-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRTQWPSPAK LNLFLYITGQ RADGYHTLQT LFQFLDYGDT ISIELRDDGD
60 70 80 90 100
IRLLTPVEGV EHEDNLIVRA ARLLMKTAAD SGRLPTGSGA NISIDKRLPM
110 120 130 140 150
GGGLGGGSSN AATVLVALNH LWQCGLSMDE LAEMGLTLGA DVPVFVRGHA
160 170 180 190 200
AFAEGVGEIL TPVDPPEKWY LVAHPGVSIP TPVIFKDPEL PRNTPKRSIE
210 220 230 240 250
TLLKCEFSND CEVIARKRFR EVDAVLSWLL EYAPSRLTGT GACVFAEFDT
260 270 280
ESEARQVLEQ APEWLNGFVA KGANLSPLHR AML
Length:283
Mass (Da):30,925
Last modified:July 19, 2004 - v1
Checksum:i59A2921FA05D13E1
GO

Sequence cautioni

The sequence BAA01106 differs from that shown. Reason: Frameshift at position 50.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti208 – 276SNDCE…GANLS → TQAYGRANTKGAPFRRTAVK CRSLGKLLLECAGKCLLRVE AVLQRDVQNRTRSQA in BAA01106 (PubMed:1427085).CuratedAdd BLAST69

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
PIRiB47706
RefSeqiNP_415726.1, NC_000913.3
WP_001260332.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC74292; AAC74292; b1208
BAA36066; BAA36066; BAA36066
GeneIDi945774
KEGGiecj:JW1199
eco:b1208
PATRICifig|1411691.4.peg.1076

Similar proteinsi

Entry informationi

Entry nameiISPE_ECOLI
AccessioniPrimary (citable) accession number: P62615
Secondary accession number(s): P24209
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: March 28, 2018
This is version 111 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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