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Protein

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

Gene

ispE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-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.

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

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Isoprene biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11294-MONOMER.
ECOL316407:JW1199-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

Protein-protein interaction databases

BioGridi4260815. 276 interactors.
DIPiDIP-48028N.
IntActiP62615. 1 interactor.
STRINGi511145.b1208.

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.
InterProiIPR013750. 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]
PANTHERiPTHR20861:SF2. PTHR20861:SF2. 1 hit.
PfamiPF08544. GHMP_kinases_C. 1 hit.
PF00288. GHMP_kinases_N. 1 hit.
[Graphical view]
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.
PATRICi32117668. VBIEscCol129921_1256.

Cross-referencesi

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.

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...

Protein-protein interaction databases

BioGridi4260815. 276 interactors.
DIPiDIP-48028N.
IntActiP62615. 1 interactor.
STRINGi511145.b1208.

Chemistry databases

ChEMBLiCHEMBL2366480.

Proteomic databases

PaxDbiP62615.
PRIDEiP62615.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74292; AAC74292; b1208.
BAA36066; BAA36066; BAA36066.
GeneIDi945774.
KEGGiecj:JW1199.
eco:b1208.
PATRICi32117668. VBIEscCol129921_1256.

Organism-specific databases

EchoBASEiEB1271.
EcoGeneiEG11294. ispE.

Phylogenomic databases

eggNOGiENOG4105CTR. Bacteria.
COG1947. LUCA.
HOGENOMiHOG000019601.
InParanoidiP62615.
KOiK00919.
OMAiRWPSPAK.
PhylomeDBiP62615.

Enzyme and pathway databases

UniPathwayiUPA00056; UER00094.
BioCyciEcoCyc:EG11294-MONOMER.
ECOL316407:JW1199-MONOMER.
MetaCyc:EG11294-MONOMER.
BRENDAi2.7.1.148. 2026.

Miscellaneous databases

PROiP62615.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.70.890. 1 hit.
HAMAPiMF_00061. IspE. 1 hit.
InterProiIPR013750. 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]
PANTHERiPTHR20861:SF2. PTHR20861:SF2. 1 hit.
PfamiPF08544. GHMP_kinases_C. 1 hit.
PF00288. GHMP_kinases_N. 1 hit.
[Graphical view]
PIRSFiPIRSF010376. IspE. 1 hit.
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55060. SSF55060. 1 hit.
TIGRFAMsiTIGR00154. ispE. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiISPE_ECOLI
AccessioniPrimary (citable) accession number: P62615
Secondary accession number(s): P24209
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: November 2, 2016
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

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

Keywords - Technical termi

3D-structure, Complete proteome, 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

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.