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Genomes and Genes | icdSummaryGene Symbol: icd Description: e14 prophage; isocitrate dehydrogenase, specific for NADP+ Alias: ECK1122, JW1122, icdA, icdE Species: Top Publications
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Publications
An SOD mimic protects NADP+-dependent isocitrate dehydrogenase against oxidative inactivationInes Batinic-Haberle
Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
Free Radic Res 42:618-24. 2008..b>ICD, however, is susceptible to oxidative inactivation, which in turn compromises cellular antioxidant defense...- Toxic waste disposal in Escherichia coliRobert B Helling
Department of Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
J Bacteriol 184:3699-703. 2002..Nal(r)) mutants in a transposition-induced library exhibited a growth factor requirement as the result of cysH, icdA, metE, or purB mutation... - Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADPS A Doyle
Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
Biochemistry 40:4234-41. 2001..In combination, these interactions appear to provide the basis for the switch in substrate specificity... - Redesigning the substrate specificity of an enzyme: isocitrate dehydrogenaseS A Doyle
Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
Biochemistry 39:14348-55. 2000..Since interactions between neighboring residues in this region greatly influenced the effects of each other in unexpected ways, structural solutions were best identified in combinations, as allowed by random mutagenesis... - Sites of binding and orientation in a four-location model for protein stereospecificityA D Mesecar
Center for Pharmaceutical Biotechnology and the Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 60607, USA
IUBMB Life 49:457-66. 2000..A four-location model is necessary to explain the enantiomeric specificity of IDH in contrast to the conventional three-point attachment model. The thermodynamic and kinetic ramifications of this model are explored... - A new model for protein stereospecificityA D Mesecar
Center for Pharmaceutical Biotechnology, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 60607, USA
Nature 403:614-5. 2000 - Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenaseD B Cherbavaz
Department of Biochemistry, University of California, San Francisco, San Francisco, CA, 94143 0448, USA
J Mol Biol 295:377-85. 2000..Comparison of K230M complexed with isocitrate and alpha-ketoglutarate illuminates the influence a ligand has on active site water structure... - Cra-dependent transcriptional activation of the icd gene of Escherichia coliJ F Prost
Institut de Biologie et Chimie des Proteines, Centre National de la Recherche Scientifique, Lyon, France
J Bacteriol 181:893-8. 1999The icd gene of Escherichia coli, encoding isocitrate dehydrogenase, was shown to be expressed from two different promoters: the previously identified icd P1 and a newly detected second promoter, icd P2, whose expression is positively .. - Access to phosphorylation in isocitrate dehydrogenase may occur by domain shiftingJ Finer-Moore
Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448, USA
Biochemistry 36:13890-6. 1997.... - Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella entericaF S Wang
Institute of Molecular Evolutionary Genetics, Mueller Laboratory, Pennsylvania State University, University Park 16802, USA
J Bacteriol 179:6551-9. 1997Sequences of the icd gene, encoding isocitrate dehydrogenase (IDH), were obtained for 33 strains representing the major phylogenetic lineages of Escherichia coli and Salmonella enterica... - Integration specificities of two lambdoid phages (21 and e14) that insert at the same attB siteH Wang
Department of Biological Sciences, Stanford University, California 94305, USA
J Bacteriol 179:5705-11. 1997It was shown previously that phage 21 and the defective element e14 integrate at the same site within the icd gene of Escherichia coli K-12 but that 21 integrase and excisionase excise e14 in vivo very infrequently compared to excision .. - Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequencesA D Mesecar
Department of Molecular and Cell Biology, Stanley Hall, University of California, Berkeley, CA 94720, USA
Science 277:202-6. 1997..The results provide evidence that orbital overlap produced by optimal orientation of reacting orbitals plays a major quantitative role in the catalytic power of enzymes... - Thermosensitive phenotype of Escherichia coli mutant lacking NADP+-dependent isocitrate dehydrogenaseIn Youl Choi
Department of Biochemistry, College of Natural Sciences, Kyungpook National University, Taegu, Korea
Redox Rep 8:51-6. 2003..These results suggest that ICDH plays an important role as an antioxidant enzyme in cellular defense against heat shock through the removal of reactive oxygen species as well as in the protection of other antioxidant enzymes... - Metabolic characteristics of an isocitrate dehydrogenase defective derivative of escherichia coli BL21(DE3)Miho Aoshima
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1 1 1, Bunkyo ku, Tokyo 113 8657, Japan
Biotechnol Bioeng 84:732-7. 2003..In addition, isocitrate lyase was not highly induced at the stationary phase. MA1935 was shown to be a good host strain for ICDH gene expression... - A common mechanism of cellular death induced by bactericidal antibioticsMichael A Kohanski
Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
Cell 130:797-810. 2007..g., reca... - Cobalt stress in Escherichia coli. The effect on the iron-sulfur proteinsCaroline Ranquet
Laboratoire de Chimie et Biologie des Metaux, iRTSV LCBM, Commissariat a l Energie Atomique CNRS Universite Joseph Fourier, CEA Grenoble, UMR 5249, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France
J Biol Chem 282:30442-51. 2007..We propose a model wherein cobalt competes out iron during synthesis of [Fe-S] clusters in metabolically essential proteins... - Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coliTadashi Ogawa
Department of Biochemistry, Aichi Medical University School of Medicine, Aichi 489 1195, Japan
J Bacteriol 189:1176-8. 2007.... - Oxidative inactivation of reduced NADP-generating enzymes in E. coli: iron-dependent inactivation with affinity cleavage of NADP-isocitrate dehydrogenaseKeiko Murakami
Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Aichi 480 1195, Japan
Arch Microbiol 186:385-92. 2006..coli... - Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenasesOlga V Kalinina
Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
Proteins 64:1001-9. 2006..coli) that contact the cofactor and may play a role in the recognition process... - Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenaseFumie Imabayashi
Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
Proteins 63:100-12. 2006..This is done to examine evolutionary relationships... - Control of isocitrate dehydrogenase catalytic activity by protein phosphorylation in Escherichia coliAlain J Cozzone
Institut de Biologie et Chimie des Proteines, Centre National de la Recherche Scientifique, Universite de Lyon, Lyon, France
J Mol Microbiol Biotechnol 9:132-46. 2005..coli and related genera on acetate and fatty acids... - The RpoS-mediated regulation of isocitrate dehydrogenase gene expression in Escherichia coliIi Lae Jung
Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, P O Box 105, Yusong, Taejon 305 600, Korea
Curr Microbiol 52:21-6. 2006The Escherichia coli NADP(+)-dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42), encoded by an icd gene, is a tricarboxylic acid (TCA) cycle enzyme responsible for the oxidative decarboxylation of isocitrate to alpha-ketoglutarate... - Genetic reconstruction of the aerobic central metabolism in Escherichia coli for the absolute aerobic production of succinateHenry Lin
Department of Bioengineering, Rice University, Houston, TX 77005, USA
Biotechnol Bioeng 89:148-56. 2005..Mutations in the tricarboxylic acid cycle (sdhAB, icd, iclR) and acetate pathways (poxB, ackA-pta) of E... - Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurementsM Mohiuddin Kabir
Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka, Japan
Appl Microbiol Biotechnol 65:84-96. 2004..how the central metabolism of Escherichia coli changes upon knockout of the isocitrate dehydrogenase (ICDH) gene (icd) in the tricarboxylic acid cycle... - Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenaseDaisuke Tsuchiya
Institute for Advanced Biosciences, Keio University, 403 1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 9970017, Japan
Biochim Biophys Acta 1784:1847-56. 2008..Connecting the two proteins by a flexible linker yielded a locally high concentration to promote the weak protein-protein interaction. The versatile architecture of AcnB may alter the metabolic process involving the Krebs cycle... - Determinants of performance in the isocitrate dehydrogenase of Escherichia coliA M Dean
Department of Biological Chemistry, Chicago Medical School, Illinois 60064 3095, USA
Protein Sci 5:341-7. 1996..These results are entirely consistent with X-ray structures of Michaelis complexes that show a hydrogen bond positions the gamma-carboxylate of isocitrate so that a salt bridge can form to the nicotinamide ring of NADP... - Second-site suppression of regulatory phosphorylation in Escherichia coli isocitrate dehydrogenaseR Chen
Department of Biological Chemistry, Chicago Medical School, Illinois 60064 3095, USA
Protein Sci 5:287-95. 1996..These movements increase the distance between the carboxylates, diminish the electrostatic repulsion, and lead to the remarkably high activity of the S113E/N115L mutant... - Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphateP E Thorsness
J Biol Chem 262:10422-5. 1987..To understand the mechanism by which phosphorylation inactivates isocitrate dehydrogenase, the sequence of icd, the isocitrate dehydrogenase structural gene, was determined and this information was used to construct mutants at .. - Excision and reintegration of the Escherichia coli K-12 chromosomal element e14H Brody
J Bacteriol 161:1112-7. 1985..We found the following sequence: fabD purB atte14 umuC. Furthermore, analysis of a recombinant plasmid that contained both the e14 attachment site and the purB locus showed that these two loci occur within 11 kilobases of each other... - Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenaseJ H Hurley
Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448
Proc Natl Acad Sci U S A 86:8635-9. 1989..Based on the structure of isocitrate dehydrogenase and conservation with isopropylmalate dehydrogenase, we suggest that the active site lies in an interdomain pocket close to the phosphorylation site... - Evidence for an arginine residue at the coenzyme-binding site of Escherichia coli isocitrate dehydrogenaseJ S McKee
Department of Biochemistry, University of Glasgow, Scotland, U K
Biochem J 261:301-4. 1989.... - Use of the isocitrate dehydrogenase structural gene for attachment of e14 in Escherichia coli K-12C W Hill
Department of Biological Chemistry, Milton S Hershey Medical Center, Pennsylvania 17033
J Bacteriol 171:4083-4. 1989The e14 element appears to be integrated into the Escherichia coli K-12 isocitrate dehydrogenase structural gene (icd). In being integrated, it replaced the last 52 codons of the gene with a closely related sequence... - Location of icdA and fadR on the physical map of Escherichia coliC Herold
Department of Microbiology, Arizona State University, Tempe 85287-2701
J Bacteriol 172:6618. 1990 - Regulation of an enzyme by phosphorylation at the active siteJ H Hurley
Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448
Science 249:1012-6. 1990..Thus, direct interaction at a ligand binding site is an alternative mechanism to induced conformational changes from an allosteric site in the regulation of protein activity by phosphorylation... - Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexesJ H Hurley
Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448
Biochemistry 30:8671-8. 1991..E. coli isocitrate dehydrogenase transfers a hydride stereospecifically to the A-side of NADP+, and models for a reactive ternary complex consistent with this stereospecificity are discussed... - Lambdoid phages as elements of bacterial genomes (integrase/phage21/Escherichia coli K-12/icd gene)A Campbell
Department of Biological Sciences, Stanford University, CA 94305
Genetica 86:259-67. 1992..We suggest that this mode of insertion arose from insertion of an ancestral phage to the right of icd which then picked up part of the icd gene by abnormal excision and speculate that, at an earlier time, phages may .. - Selection for citrate synthase deficiency in icd mutants of Escherichia coliT M Lakshmi
J Bacteriol 127:76-83. 1976Cultures of isocitrate dehydrogenase-deficient (icd) mutants were overgrown by double mutants (icd glt) lacking citrate synthase activity also... - A highly active decarboxylating dehydrogenase with rationally inverted coenzyme specificityR Chen
Department of Biological Chemistry, Chicago Medical School, North Chicago, IL 60064, USA
Proc Natl Acad Sci U S A 92:11666-70. 1995..Two additional mutations at remote sites improve performance further, resulting in a final mutant enzyme with kinetic characteristics and coenzyme preference comparable to naturally occurring homologous NAD-dependent enzymes... - Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenaseJ M Bolduc
Fred Hutchinson Cancer Research Center, Program in Structural Biology, Seattle, WA 98104, USA
Science 268:1312-8. 1995..Mutation of key catalytic residues changed the rate determining steps so that protein and substrate intermediates within the overall reaction pathway could be visualized... - Determinants of cofactor specificity in isocitrate dehydrogenase: structure of an engineered NADP+ --> NAD+ specificity-reversal mutantJ H Hurley
Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0580, USA
Biochemistry 35:5670-8. 1996..The side chain of this "second layer" residue dictates packing of the surrounding "first layer" residues which interact with the 2' moiety and, in turn, directly determine specificity... - The phosphorylation of Escherichia coli isocitrate dehydrogenase in intact cellsA C Borthwick
Biochem J 222:797-804. 1984..Only one phosphopeptide was observed in each case; the results show that the residue phosphorylated in vivo is identical with that phosphorylated by purified isocitrate dehydrogenase kinase in vitro... - Nalidixic acd-resistant mutants of Escherichia coli deficient in isocitrate dehydrogenaseR B Helling
J Bacteriol 105:1224-6. 1971b>icd Mutants of Escherichia coli K-12, selected for their resistance to nalidixic acid, are deficient in isocitrate dehydrogenase. - Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrateB L Stoddard
Department of Molecular and Cellular Biology, University of California, Berkeley 94720
Biochemistry 32:9317-22. 1993.... - Structure of isocitrate dehydrogenase with isocitrate, nicotinamide adenine dinucleotide phosphate, and calcium at 2.5-A resolution: a pseudo-Michaelis ternary complexB L Stoddard
Department of Molecular and Cellular Biology, University of California, Berkeley 94720
Biochemistry 32:9310-6. 1993..iv) The orientation and interactions of the nicotinamide ring with the substrate are consistent with the stereospecificity of the enzyme-catalyzed reaction... - Regulation of isocitrate dehydrogenase by phosphorylation involves no long-range conformational change in the free enzymeJ H Hurley
Department of Biochemistry and Biophysics, University of California, San Francisco 94143 0448
J Biol Chem 265:3599-602. 1990.... - Analysis of the lambdoid prophage element e14 in the E. coli K-12 genomePreeti Mehta
Bioinformatics Centre, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, India
BMC Microbiol 4:4. 2004..coli K-12 genome. This prophage encodes important functional genes such as lit (T4 exclusion), mcrA (modified cytosine restriction activity) and pin (recombinase)...
Research Grants
- Small Molecule X-Ray Diffraction InstrumentationAndrew Mesecar; Fiscal Year: 2002..abstract_text> ..
- A Molecular Basis for Phytoestrogen ChemopreventionAndrew Mesecar; Fiscal Year: 2002..aid in the design of new compounds that can serve as selective estrogen modulators (SERMs). ..
- Macromolecular X-ray Structure Facility InstrumentationAndrew Mesecar; Fiscal Year: 2003....
- Novel Organophosphorous Hydrolases for DecontaminationAndrew Mesecar; Fiscal Year: 2007..In Phase II, we propose to develop large-scale production and purification processes for the enzyme, and to further enhance the catalytic activity of the enzyme towards the V-agents using directed-evolution approaches. ..