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Gene Review

icd  -  isocitrate dehydrogenase; e14 prophage...

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK1122, JW1122, icdA, icdE
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Disease relevance of icd


High impact information on icd


Chemical compound and disease context of icd


Biological context of icd

  • The upregulation of icdA gene may be due to the positive regulation of fruR [1].
  • The enzyme activities of both ICDH, found to be NAD+ dependent, and citrate synthase were measured in cell extracts of wild-type S. mutans and E. coli mutants harboring plasmid pJG400 [15].
  • Moreover, the main metabolic pathways and carbon flow operating during cell biotransformation was that controlled by the ICDH/ICL ratio, which decreased from 8.0 to 2.5, and the phosphotransferase/ACS ratio, which increased from 2.1 to 5.2, after a NaCl pulse fivefold the steady-state level [16].
  • Southern hybridization using cDNA-1 and cDNA-2 indicated that there is only one copy of icdA on the chromosomes of A. niger WU-2223L [17].
  • The chromosomal DNA, icdA, was cloned to correspond to cDNA-1, and its nucleotide sequence revealed that it contains seven introns [17].

Anatomical context of icd

  • 7. IDH activity was detected in the complemented E. coli strain and the electrophoretic mobility of this activity in nondenaturing polyacrylamide gels was identical to that of an IDH in extracts from soybean cotyledons or nodule cytosol [18].
  • Expression of full-length ICDH generated recombinant protein exclusively expressed in inclusion bodies but the removal of 27 N-terminal amino acids yielded appreciable amounts of soluble ICDH consistent with the prediction that these residues confer targeting of the native protein to the parasites' mitochondrion [19].
  • Effects of long-chain acyl-coenzyme A's on the activity of the soluble form of nicotinamide adenine dinucleotide phosphate-specific isocitrate dehydrogenase from lactating bovine mammary gland [20].
  • Molecular cloning of the cDNA of mouse mitochondrial NADP-dependent isocitrate dehydrogenase and the expression of the gene during lymphocyte activation [21].
  • Bradyrhizobium japonicum NADP(+)-dependent isocitrate dehydrogenase was purified both from cultured cells and from the symbiotic form of the bacteria and was found to be identical in terms of N-terminal amino acid sequence, kinetics, and physicochemical properties [22].

Associations of icd with chemical compounds


Regulatory relationships of icd


Other interactions of icd

  • Based on the aforementioned criteria, the icd (isocitrate dehydrogenase), and putP (proline permease) genes were excluded as potential targets due to their high rates of horizontal gene transfer; the rrs (16S rRNA) gene was excluded as a target due to the presence of multiple gene copies, with different sequences in a single genome [26].
  • The results are strikingly similar to previous results reported on the nicotinamide adenine dinucleotide (NAD+) dependent malic enzyme and the NAD+-dependent isocitrate dehydrogenase, supporting the suggestion that metal cofactors function as regulatory entities [27].

Analytical, diagnostic and therapeutic context of icd


  1. Gene expression patterns for metabolic pathway in pgi knockout Escherichia coli with and without phb genes based on RT-PCR. Kabir, M.M., Shimizu, K. J. Biotechnol. (2003) [Pubmed]
  2. Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica. Wang, F.S., Whittam, T.S., Selander, R.K. J. Bacteriol. (1997) [Pubmed]
  3. Cloning and mutagenesis of the Rhizobium meliloti isocitrate dehydrogenase gene. McDermott, T.R., Kahn, M.L. J. Bacteriol. (1992) [Pubmed]
  4. Two phenotypically compensating isocitrate dehydrogenases in Ralstonia eutropha. Wang, Z.X., Brämer, C., Steinbüchel, A. FEMS Microbiol. Lett. (2003) [Pubmed]
  5. Crystal structure of Bacillus subtilis isocitrate dehydrogenase at 1.55 A. Insights into the nature of substrate specificity exhibited by Escherichia coli isocitrate dehydrogenase kinase/phosphatase. Singh, S.K., Matsuno, K., LaPorte, D.C., Banaszak, L.J. J. Biol. Chem. (2001) [Pubmed]
  6. Electrostatic and steric contributions to regulation at the active site of isocitrate dehydrogenase. Dean, A.M., Koshland, D.E. Science (1990) [Pubmed]
  7. Immunochemical localization of NADP-specific isocitrate dehydrogenase in Escherichia coli. Swafford, J.R., Malloy, P.J., Reeves, H.C. Science (1983) [Pubmed]
  8. Phosphorylation of Isocitrate dehydrogenase of Escherichia coli. Garnak, M., Reeves, H.C. Science (1979) [Pubmed]
  9. Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli. Stoddard, B.L., Koshland, D.E. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  10. Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. Hurley, J.H., Thorsness, P.E., Ramalingam, V., Helmers, N.H., Koshland, D.E., Stroud, R.M. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  11. Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes. Hurley, J.H., Dean, A.M., Koshland, D.E., Stroud, R.M. Biochemistry (1991) [Pubmed]
  12. Compensatory phosphorylation of isocitrate dehydrogenase. A mechanism for adaptation to the intracellular environment. LaPorte, D.C., Thorsness, P.E., Koshland, D.E. J. Biol. Chem. (1985) [Pubmed]
  13. Phosphorylation inactivates Escherichia coli isocitrate dehydrogenase by preventing isocitrate binding. Dean, A.M., Lee, M.H., Koshland, D.E. J. Biol. Chem. (1989) [Pubmed]
  14. Identification by mutagenesis of arginines in the substrate binding site of the porcine NADP-dependent isocitrate dehydrogenase. Soundar, S., Danek, B.L., Colman, R.F. J. Biol. Chem. (2000) [Pubmed]
  15. Role of the citrate pathway in glutamate biosynthesis by Streptococcus mutans. Cvitkovitch, D.G., Gutierrez, J.A., Bleiweis, A.S. J. Bacteriol. (1997) [Pubmed]
  16. Salt stress effects on the central and carnitine metabolisms of Escherichia coli. Cánovas, M., Bernal, V., Sevilla, A., Iborra, J.L. Biotechnol. Bioeng. (2007) [Pubmed]
  17. Cloning and expression of Aspergillus niger icdA gene encoding mitochondrial NADP+-specific isocitrate dehydrogenase. Kirimura, K., Yoda, M., Kumatani, M., Ishii, Y., Kino, K., Usami, S. J. Biosci. Bioeng. (2002) [Pubmed]
  18. Isolation and characterization of a cDNA encoding NADP(+)-specific isocitrate dehydrogenase from soybean (Glycine max). Udvardi, M.K., McDermott, T.R., Kahn, M.L. Plant Mol. Biol. (1993) [Pubmed]
  19. Isocitrate dehydrogenase of Plasmodium falciparum. Wrenger, C., Müller, S. Eur. J. Biochem. (2003) [Pubmed]
  20. Effects of long-chain acyl-coenzyme A's on the activity of the soluble form of nicotinamide adenine dinucleotide phosphate-specific isocitrate dehydrogenase from lactating bovine mammary gland. Farrell, H.M., Wickham, E.D., Reeves, H.C. Arch. Biochem. Biophys. (1995) [Pubmed]
  21. Molecular cloning of the cDNA of mouse mitochondrial NADP-dependent isocitrate dehydrogenase and the expression of the gene during lymphocyte activation. Yang, L., Luo, H., Vinay, P., Wu, J. J. Cell. Biochem. (1996) [Pubmed]
  22. Bradyrhizobium japonicum isocitrate dehydrogenase exhibits calcium-dependent hysteresis. Karr, D.B., Emerich, D.W. Arch. Biochem. Biophys. (2000) [Pubmed]
  23. Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate. Thorsness, P.E., Koshland, D.E. J. Biol. Chem. (1987) [Pubmed]
  24. Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. Cherbavaz, D.B., Lee, M.E., Stroud, R.M., Koshland, D.E. J. Mol. Biol. (2000) [Pubmed]
  25. Compensatory regulation in metabolic pathways--responses to increases and decreases in citrate synthase levels. Walsh, K., Schena, M., Flint, A.J., Koshland, D.E. Biochem. Soc. Symp. (1987) [Pubmed]
  26. Microbial source tracking by DNA sequence analysis of the Escherichia coli malate dehydrogenase gene. Ivanetich, K.M., Hsu, P.H., Wunderlich, K.M., Messenger, E., Walkup, W.G., Scott, T.M., Lukasik, J., Davis, J. J. Microbiol. Methods (2006) [Pubmed]
  27. Role of metal cofactors in enzyme regulation. Differences in the regulatory properties of the Escherichia coli nicotinamide adenine dinucleotide phosphate specific malic enzyme, depending on whether magnesium ion or manganese ion serves as divalent cation. Brown, D.A., Cook, R.A. Biochemistry (1981) [Pubmed]
  28. Sites of binding and orientation in a four-location model for protein stereospecificity. Mesecar, A.D., Koshland, D.E. IUBMB Life (2000) [Pubmed]
  29. Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase. Dean, A.M., Golding, G.B. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  30. Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase. Soundar, S., O'hagan, M., Fomulu, K.S., Colman, R.F. J. Biol. Chem. (2006) [Pubmed]
  31. Evaluation by site-directed mutagenesis of aspartic acid residues in the metal site of pig heart NADP-dependent isocitrate dehydrogenase. Grodsky, N.B., Soundar, S., Colman, R.F. Biochemistry (2000) [Pubmed]
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