Identification
Name:Isocitrate dehydrogenase [NADP]
Synonyms:
  • IDH
  • IDP
  • NADP(+)-specific ICDH
  • Oxalosuccinate decarboxylase
Gene Name:icd
Enzyme Class:
Biological Properties
General Function:Involved in magnesium ion binding
Specific Function:Isocitrate + NADP(+) = 2-oxoglutarate + CO(2) + NADPH
Cellular Location:Not Available
SMPDB Pathways:
KEGG Pathways:
KEGG Reactions:
Thumb+ThumbThumb+Thumb+Thumb
Thumb+ThumbThumb+Thumb+Thumb+Thumb
ThumbThumb+Thumb
Thumb+ThumbThumb+Thumb+Thumb
Thumb+ThumbThumb+Thumb+Thumb
Thumb+Thumb+ThumbThumb+Thumb+Thumb+Thumb
SMPDB Reactions:
Thumb+ThumbThumb+NADPH+Thumb+Thumb
EcoCyc Reactions:
Thumb+ThumbThumb+Thumb+Thumb
Thumb+ThumbThumb+Thumb+Thumb
Metabolites:
ECMDB IDNameView
ECMDB02812alpha-KetoglutarateMetaboCard
ECMDB04030Carbon dioxideMetaboCard
ECMDB24074D-threo-Isocitric acidMetaboCard
ECMDB21225Hydrogen ionMetaboCard
ECMDB04088Isocitric acidMetaboCard
ECMDB00217NADPMetaboCard
ECMDB04111NADPHMetaboCard
ECMDB03974Oxalosuccinic acidMetaboCard
ECMDB04123Oxoglutaric acidMetaboCard
GO Classification:
Function
binding
catalytic activity
cation binding
ion binding
isocitrate dehydrogenase (NADP+) activity
isocitrate dehydrogenase activity
magnesium ion binding
metal ion binding
NAD or NADH binding
nucleotide binding
oxidoreductase activity
oxidoreductase activity, acting on CH-OH group of donors
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Process
acetyl-CoA catabolic process
acetyl-CoA metabolic process
cellular metabolic process
coenzyme metabolic process
cofactor metabolic process
metabolic process
oxidation reduction
tricarboxylic acid cycle
Gene Properties
Blattner:b1136
Gene OrientationClockwise
Centisome Percentage:25.74
Left Sequence End1194346
Right Sequence End1195596
Gene Sequence:
>1212 bp
GGCAAGAAGATCACCCTGCAAAACGGCAAACTCAACGTTCCTGAAAATCCGATTATCCCT
TACATTGAAGGTGATGGAATCGGTGTAGATGTAACCCCAGCCATGCTGAAAGTGGTCGAC
GCTGCAGTCGAGAAAGCCTATAAAGGCGAGCGTAAAATCTCCTGGATGGAAATTTACACC
GGTGAAAAATCCACACAGGTTTATGGTCAGGACGTCTGGCTGCCTGCTGAAACTCTTGAT
CTGATTCGTGAATATCGCGTTGCCATTAAAGGTCCGCTGACCACTCCGGTTGGTGGCGGT
ATTCGCTCTCTGAACGTTGCCCTGCGCCAGGAACTGGATCTCTACATCTGCCTGCGTCCG
GTACGTTACTATCAGGGCACTCCAAGCCCGGTTAAACACCCTGAACTGACCGATATGGTT
ATCTTCCGTGAAAACTCGGAAGACATTTATGCGGGTATCGAATGGAAAGCAGACTCTGCC
GACGCCGAGAAAGTGATTAAATTCCTGCGTGAAGAGATGGGGGTGAAGAAAATTCGCTTC
CCGGAACATTGTGGTATCGGTATTAAGCCGTGTTCGGAAGAAGGCACCAAACGTCTGGTT
CGTGCAGCGATCGAATACGCAATTGCTAACGATCGTGACTCTGTGACTCTGGTGCACAAA
GGCAACATCATGAAGTTCACCGAAGGAGCGTTTAAAGACTGGGGCTACCAGCTGGCGCGT
GAAGAGTTTGGCGGTGAACTGATCGACGGTGGCCCGTGGCTGAAAGTTAAAAACCCGAAC
ACTGGCAAAGAGATCGTCATTAAAGACGTGATTGCTGATGCATTCCTGCAACAGATCCTG
CTGCGTCCGGCTGAATATGATGTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCT
GACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGAC
GAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAA
GTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACC
GAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACC
TATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAC
GCGATCATCGAA
Protein Properties
Pfam Domain Function:
Protein Residues:416
Protein Molecular Weight:45756
Protein Theoretical pI:5
PDB File:1PB3
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Isocitrate dehydrogenase [NADP]
MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGE
RKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQ
ELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLR
EEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGA
FKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIA
CMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSA
EMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM
References
External Links:
ResourceLink
Uniprot ID:P08200
Uniprot Name:IDH_ECOLI
GenBank Gene ID:AF017587
Genebank Protein ID:2618876
PDB ID:1PB3
Ecogene ID:EG10489
Ecocyc:EG10489
ColiBase:b1136
Kegg Gene:b1136
EchoBASE ID:EB0484
CCDB:IDH_ECOLI
BacMap:16129099
General Reference:
  • Blattner, F. R., Plunkett, G. 3rd, 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. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Bolduc, J. M., Dyer, D. H., Scott, W. G., Singer, P., Sweet, R. M., Koshland, D. E. Jr, Stoddard, B. L. (1995). "Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase." Science 268:1312-1318. Pubmed: 7761851
  • Cherbavaz, D. B., Lee, M. E., Stroud, R. M., Koshland, D. E. Jr (2000). "Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase." J Mol Biol 295:377-385. Pubmed: 10623532
  • Doyle, S. A., Beernink, P. T., Koshland, D. E. Jr (2001). "Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP." Biochemistry 40:4234-4241. Pubmed: 11284679
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Hurley, J. H., Dean, A. M., Sohl, J. L., Koshland, D. E. Jr, Stroud, R. M. (1990). "Regulation of an enzyme by phosphorylation at the active site." Science 249:1012-1016. Pubmed: 2204109
  • Hurley, J. H., Thorsness, P. E., Ramalingam, V., Helmers, N. H., Koshland, D. E. Jr, Stroud, R. M. (1989). "Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase." Proc Natl Acad Sci U S A 86:8635-8639. Pubmed: 2682654
  • Lee, M. E., Dyer, D. H., Klein, O. D., Bolduc, J. M., Stoddard, B. L., Koshland, D. E. Jr (1995). "Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli." Biochemistry 34:378-384. Pubmed: 7819221
  • Link, A. J., Robison, K., Church, G. M. (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18:1259-1313. Pubmed: 9298646
  • 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., Horiuchi, T., et, a. l. .. (1996). "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." DNA Res 3:137-155. Pubmed: 8905232
  • Thorsness, P. E., Koshland, D. E. Jr (1987). "Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate." J Biol Chem 262:10422-10425. Pubmed: 3112144
  • Wang, F. S., Whittam, T. S., Selander, R. K. (1997). "Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica." J Bacteriol 179:6551-6559. Pubmed: 9352899
  • Zhang, J., Sprung, R., Pei, J., Tan, X., Kim, S., Zhu, H., Liu, C. F., Grishin, N. V., Zhao, Y. (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8:215-225. Pubmed: 18723842