ID ISPE_ECOLI Reviewed; 283 AA.
AC P62615; P24209;
DT 19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 24-JAN-2024, entry version 141.
DE RecName: Full=4-diphosphocytidyl-2-C-methyl-D-erythritol kinase;
DE Short=CMK;
DE EC=2.7.1.148 {ECO:0000269|PubMed:10570138, ECO:0000269|PubMed:10655484, ECO:0000269|Ref.6};
DE AltName: Full=4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase;
GN Name=ispE; Synonyms=ipk, ychB {ECO:0000303|PubMed:10570138};
GN OrderedLocusNames=b1208, JW1199;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1427085; DOI=10.1016/0378-1119(92)90170-t;
RA Ikemi M., Murakami K., Hashimoto M., Murooka Y.;
RT "Cloning and characterization of genes involved in the biosynthesis of
RT delta-aminolevulinic acid in Escherichia coli.";
RL Gene 121:127-132(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=7679718; DOI=10.1099/00221287-139-2-259;
RA Post D.A., Hove-Jensen B., Switzer R.L.;
RT "Characterization of the hemA-prs region of the Escherichia coli and
RT Salmonella typhimurium chromosomes: identification of two open reading
RT frames and implications for prs expression.";
RL J. Gen. Microbiol. 139:259-266(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=7543480; DOI=10.1128/jb.177.15.4488-4500.1995;
RA Strohmaier H., Remler P., Renner W., Hoegenauer G.;
RT "Expression of genes kdsA and kdsB involved in 3-deoxy-D-manno-octulosonic
RT acid metabolism and biosynthesis of enterobacterial lipopolysaccharide is
RT growth phase regulated primarily at the transcriptional level in
RT Escherichia coli K-12.";
RL J. Bacteriol. 177:4488-4500(1995).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP PATHWAY.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=10570138; DOI=10.1073/pnas.96.24.13714;
RA Lange B.M., Croteau R.;
RT "Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway:
RT isopentenyl monophosphate kinase catalyzes the terminal enzymatic step.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:13714-13719(1999).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=10655484; DOI=10.1073/pnas.97.3.1062;
RA Luettgen H., Rohdich F., Herz S., Wungsintaweekul J., Hecht S.,
RA Schuhr C.A., Fellermeier M., Sagner S., Zenk M.H., Bacher A.,
RA Eisenreich W.;
RT "Biosynthesis of terpenoids: YchB protein of Escherichia coli
RT phosphorylates the 2-hydroxy group of 4-diphosphocytidyl-2C-methyl-D-
RT erythritol.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:1062-1067(2000).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Kuzuyama T., Takagi M., Kaneda K., Watanabe H., Dairi T., Seto H.;
RT "Studies on the nonmevalonate pathway: conversion of 4-(cytidine 5'-
RT diphospho)-2-C-methyl-D-erythritol to its 2-phospho derivative by 4-
RT (cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase.";
RL Tetrahedron Lett. 41:2925-2928(2000).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [9]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [10]
RP MUTAGENESIS OF GLY-239 AND THR-240.
RX PubMed=12859972; DOI=10.1016/s0006-291x(03)01211-7;
RA Sauret-Gueeto S., Ramos-Valdivia A., Ibanez E., Boronat A.,
RA Rodriguez-Concepcion M.;
RT "Identification of lethal mutations in Escherichia coli genes encoding
RT enzymes of the methylerythritol phosphate pathway.";
RL Biochem. Biophys. Res. Commun. 307:408-415(2003).
CC -!- FUNCTION: Catalyzes the phosphorylation of the position 2 hydroxy group
CC of 4-diphosphocytidyl-2C-methyl-D-erythritol (PubMed:10570138,
CC PubMed:10655484, Ref.6). Phosphorylates isopentenyl phosphate at low
CC rates. Also acts on isopentenol, and, much less efficiently,
CC dimethylallyl alcohol. Dimethylallyl monophosphate does not serve as a
CC substrate (PubMed:10570138). {ECO:0000269|PubMed:10570138,
CC ECO:0000269|PubMed:10655484, ECO:0000269|Ref.6}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-
CC erythritol 2-phosphate + ADP + H(+); Xref=Rhea:RHEA:18437,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:57823,
CC ChEBI:CHEBI:57919, ChEBI:CHEBI:456216; EC=2.7.1.148;
CC Evidence={ECO:0000269|PubMed:10570138, ECO:0000269|PubMed:10655484,
CC ECO:0000269|Ref.6};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18438;
CC Evidence={ECO:0000269|PubMed:10570138, ECO:0000269|PubMed:10655484,
CC ECO:0000269|Ref.6};
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC phosphate: step 3/6. {ECO:0000305|PubMed:10570138}.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- INTERACTION:
CC P62615; P17169: glmS; NbExp=2; IntAct=EBI-562202, EBI-551022;
CC -!- SIMILARITY: Belongs to the GHMP kinase family. IspE subfamily.
CC {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be an isopentenyl monophosphate
CC kinase. {ECO:0000305|PubMed:1427085}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA01106.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; D10264; BAA01106.1; ALT_FRAME; Genomic_DNA.
DR EMBL; M77237; AAA24434.1; -; Genomic_DNA.
DR EMBL; U18555; AAC43434.1; -; Genomic_DNA.
DR EMBL; AJ249325; CAB64963.1; -; Genomic_DNA.
DR EMBL; AF179284; AAF13867.1; -; Genomic_DNA.
DR EMBL; AF216300; AAF29530.1; -; Genomic_DNA.
DR EMBL; AB037116; BAA94247.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74292.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA36066.1; -; Genomic_DNA.
DR PIR; B47706; B47706.
DR RefSeq; NP_415726.1; NC_000913.3.
DR RefSeq; WP_001260332.1; NZ_SSZK01000010.1.
DR PDB; 2WW4; X-ray; 2.00 A; A/B=1-283.
DR PDBsum; 2WW4; -.
DR AlphaFoldDB; P62615; -.
DR SMR; P62615; -.
DR BioGRID; 4260815; 299.
DR DIP; DIP-48028N; -.
DR IntAct; P62615; 1.
DR STRING; 511145.b1208; -.
DR BindingDB; P62615; -.
DR ChEMBL; CHEMBL2366480; -.
DR jPOST; P62615; -.
DR PaxDb; 511145-b1208; -.
DR EnsemblBacteria; AAC74292; AAC74292; b1208.
DR GeneID; 945774; -.
DR KEGG; ecj:JW1199; -.
DR KEGG; eco:b1208; -.
DR PATRIC; fig|1411691.4.peg.1076; -.
DR EchoBASE; EB1271; -.
DR eggNOG; COG1947; Bacteria.
DR HOGENOM; CLU_053057_3_0_6; -.
DR InParanoid; P62615; -.
DR OMA; RWPSPAK; -.
DR OrthoDB; 9809438at2; -.
DR PhylomeDB; P62615; -.
DR BioCyc; EcoCyc:EG11294-MONOMER; -.
DR BioCyc; MetaCyc:EG11294-MONOMER; -.
DR BRENDA; 2.7.1.148; 2026.
DR UniPathway; UPA00056; UER00094.
DR PRO; PR:P62615; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0050515; F:4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IDA:EcoCyc.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEA:UniProtKB-UniPathway.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.70.890; GHMP kinase, C-terminal domain; 1.
DR HAMAP; MF_00061; IspE; 1.
DR InterPro; IPR013750; GHMP_kinase_C_dom.
DR InterPro; IPR036554; GHMP_kinase_C_sf.
DR InterPro; IPR006204; GHMP_kinase_N_dom.
DR InterPro; IPR004424; IspE.
DR InterPro; IPR020568; Ribosomal_Su5_D2-typ_SF.
DR InterPro; IPR014721; Ribsml_uS5_D2-typ_fold_subgr.
DR NCBIfam; TIGR00154; ispE; 1.
DR PANTHER; PTHR43527; 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE, CHLOROPLASTIC; 1.
DR PANTHER; PTHR43527:SF2; 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE, CHLOROPLASTIC; 1.
DR Pfam; PF08544; GHMP_kinases_C; 1.
DR Pfam; PF00288; GHMP_kinases_N; 1.
DR PIRSF; PIRSF010376; IspE; 1.
DR SUPFAM; SSF55060; GHMP Kinase, C-terminal domain; 1.
DR SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Isoprene biosynthesis; Kinase;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..283
FT /note="4-diphosphocytidyl-2-C-methyl-D-erythritol kinase"
FT /id="PRO_0000189215"
FT ACT_SITE 10
FT /evidence="ECO:0000250"
FT ACT_SITE 141
FT /evidence="ECO:0000250"
FT BINDING 99..109
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT MUTAGEN 239
FT /note="G->R: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12859972"
FT MUTAGEN 240
FT /note="T->I: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12859972"
FT CONFLICT 208..276
FT /note="SNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLE
FT QAPEWLNGFVAKGANLS -> TQAYGRANTKGAPFRRTAVKCRSLGKLLLECAGKCLLR
FT VEAVLQRDVQNRTRSQA (in Ref. 1; BAA01106)"
FT /evidence="ECO:0000305"
FT STRAND 2..20
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 26..49
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 66..80
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 89..95
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 106..121
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 128..136
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 142..147
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:2WW4"
FT TURN 155..158
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 159..162
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 181..185
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 199..203
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 212..218
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 220..230
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 235..237
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 244..250
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 251..260
FT /evidence="ECO:0007829|PDB:2WW4"
FT STRAND 267..275
FT /evidence="ECO:0007829|PDB:2WW4"
FT HELIX 277..281
FT /evidence="ECO:0007829|PDB:2WW4"
SQ SEQUENCE 283 AA; 30925 MW; 59A2921FA05D13E1 CRC64;
MRTQWPSPAK LNLFLYITGQ RADGYHTLQT LFQFLDYGDT ISIELRDDGD IRLLTPVEGV
EHEDNLIVRA ARLLMKTAAD SGRLPTGSGA NISIDKRLPM GGGLGGGSSN AATVLVALNH
LWQCGLSMDE LAEMGLTLGA DVPVFVRGHA AFAEGVGEIL TPVDPPEKWY LVAHPGVSIP
TPVIFKDPEL PRNTPKRSIE TLLKCEFSND CEVIARKRFR EVDAVLSWLL EYAPSRLTGT
GACVFAEFDT ESEARQVLEQ APEWLNGFVA KGANLSPLHR AML
//
