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P62615

- ISPE_ECOLI

UniProt

P62615 - ISPE_ECOLI

Protein

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

Gene

ispE

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 1 (19 Jul 2004)
      Previous versions | rss
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    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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei10 – 101By similarity
    Active sitei141 – 1411By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi99 – 10911ATPSequence AnalysisAdd
    BLAST

    GO - Molecular functioni

    1. 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity Source: EcoCyc
    2. ATP binding Source: EcoCyc

    GO - Biological processi

    1. isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Source: UniProtKB-UniPathway
    2. terpenoid biosynthetic process Source: UniProtKB-HAMAP
    3. ubiquinone biosynthetic process Source: EcoCyc

    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.
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11294. ispE.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi239 – 2391G → R: Loss of activity. 1 Publication
    Mutagenesisi240 – 2401T → I: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2832834-diphosphocytidyl-2-C-methyl-D-erythritol kinasePRO_0000189215Add
    BLAST

    Proteomic databases

    PaxDbiP62615.

    Expressioni

    Gene expression databases

    GenevestigatoriP62615.

    Interactioni

    Subunit structurei

    Homodimer.By similarity

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    glmSP171691EBI-562202,EBI-551022

    Protein-protein interaction databases

    DIPiDIP-48028N.
    IntActiP62615. 1 interaction.
    STRINGi511145.b1208.

    Structurei

    Secondary structure

    1
    283
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 2019
    Beta strandi26 – 4924
    Beta strandi51 – 533
    Helixi62 – 643
    Helixi66 – 8015
    Beta strandi89 – 957
    Helixi106 – 12116
    Helixi128 – 1369
    Helixi142 – 1476
    Beta strandi151 – 1544
    Turni155 – 1584
    Beta strandi159 – 1624
    Beta strandi169 – 1735
    Helixi181 – 1855
    Helixi199 – 2035
    Helixi212 – 2187
    Helixi220 – 23011
    Beta strandi235 – 2373
    Beta strandi244 – 2507
    Helixi251 – 26010
    Beta strandi267 – 2759
    Helixi277 – 2815

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2WW4X-ray2.00A/B1-283[»]
    ProteinModelPortaliP62615.
    SMRiP62615. Positions 1-282.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the GHMP kinase family. IspE subfamily.Curated

    Phylogenomic databases

    eggNOGiCOG1947.
    HOGENOMiHOG000019601.
    KOiK00919.
    OMAiVSTAEIF.
    OrthoDBiEOG62VNQ2.
    PhylomeDBiP62615.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.30.70.890. 1 hit.
    HAMAPiMF_00061. IspE.
    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

    MRTQWPSPAK LNLFLYITGQ RADGYHTLQT LFQFLDYGDT ISIELRDDGD    50
    IRLLTPVEGV EHEDNLIVRA ARLLMKTAAD SGRLPTGSGA NISIDKRLPM 100
    GGGLGGGSSN AATVLVALNH LWQCGLSMDE LAEMGLTLGA DVPVFVRGHA 150
    AFAEGVGEIL TPVDPPEKWY LVAHPGVSIP TPVIFKDPEL PRNTPKRSIE 200
    TLLKCEFSND CEVIARKRFR EVDAVLSWLL EYAPSRLTGT GACVFAEFDT 250
    ESEARQVLEQ APEWLNGFVA KGANLSPLHR AML 283
    Length:283
    Mass (Da):30,925
    Last modified:July 19, 2004 - v1
    Checksum:i59A2921FA05D13E1
    GO

    Sequence cautioni

    The sequence BAA01106.1 differs from that shown. Reason: Frameshift at position 50.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti208 – 27669SNDCE…GANLS → TQAYGRANTKGAPFRRTAVK CRSLGKLLLECAGKCLLRVE AVLQRDVQNRTRSQA in BAA01106. (PubMed:1427085)CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_489475.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74292; AAC74292; b1208.
    BAA36066; BAA36066; BAA36066.
    GeneIDi12931821.
    945774.
    KEGGiecj:Y75_p1180.
    eco:b1208.
    PATRICi32117668. VBIEscCol129921_1256.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi B47706.
    RefSeqi NP_415726.1. NC_000913.3.
    YP_489475.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2WW4 X-ray 2.00 A/B 1-283 [» ]
    ProteinModelPortali P62615.
    SMRi P62615. Positions 1-282.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48028N.
    IntActi P62615. 1 interaction.
    STRINGi 511145.b1208.

    Proteomic databases

    PaxDbi P62615.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74292 ; AAC74292 ; b1208 .
    BAA36066 ; BAA36066 ; BAA36066 .
    GeneIDi 12931821.
    945774.
    KEGGi ecj:Y75_p1180.
    eco:b1208.
    PATRICi 32117668. VBIEscCol129921_1256.

    Organism-specific databases

    EchoBASEi EB1271.
    EcoGenei EG11294. ispE.

    Phylogenomic databases

    eggNOGi COG1947.
    HOGENOMi HOG000019601.
    KOi K00919.
    OMAi VSTAEIF.
    OrthoDBi EOG62VNQ2.
    PhylomeDBi P62615.

    Enzyme and pathway databases

    UniPathwayi UPA00056 ; UER00094 .
    BioCyci EcoCyc:EG11294-MONOMER.
    ECOL316407:JW1199-MONOMER.
    MetaCyc:EG11294-MONOMER.

    Miscellaneous databases

    PROi P62615.

    Gene expression databases

    Genevestigatori P62615.

    Family and domain databases

    Gene3Di 3.30.230.10. 1 hit.
    3.30.70.890. 1 hit.
    HAMAPi MF_00061. IspE.
    InterProi 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 ]
    PANTHERi PTHR20861:SF2. PTHR20861:SF2. 1 hit.
    Pfami PF08544. GHMP_kinases_C. 1 hit.
    PF00288. GHMP_kinases_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF010376. IspE. 1 hit.
    SUPFAMi SSF54211. SSF54211. 1 hit.
    SSF55060. SSF55060. 1 hit.
    TIGRFAMsi TIGR00154. ispE. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    8. 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.

    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: October 1, 2014
    This is version 91 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

    External Data

    Dasty 3