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    icd isocitrate dehydrogenase [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 945702, updated on 3-Dec-2024

    Summary

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    Official Symbol
    icd
    Official Full Name
    isocitrate dehydrogenase
    Primary source
    ECOCYC:EG10489
    Locus tag
    b1136
    See related
    ASAP:ABE-0003823
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK1122; icdA; icdE
    Summary
    This icd allele has a C-terminus added during prophage e14 integration at codon 362, introducing 2 amino acid changes in icd. icdC encodes the original C-terminus of icd. [More information is available at EcoGene: EG10489]. There are marked differences in the properties of enzymes from different sources. [More information is available at EcoCyc: EG10489].
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    Genomic context

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    Sequence:
    NC_000913.3 (1195123..1196373)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene phosphatase NudJ Neighboring gene 23S rRNA pseudouridine(2457) synthase Neighboring gene ncRNA Neighboring gene putative SAM-dependent methyltransferase YmfD

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Determinants of cofactor specificity in isocitrate dehydrogenase: structure of an engineered NADP+ --> NAD+ specificity-reversal mutant. Hurley JH, et al. Biochemistry, 1996 May 7. PMID 8639526
    2. Metabolic characteristics of an isocitrate dehydrogenase defective derivative of escherichia coli BL21(DE3). Aoshima M, et al. Biotechnol Bioeng, 2003 Dec 20. PMID 14595786
    3. Thermosensitive phenotype of Escherichia coli mutant lacking NADP+-dependent isocitrate dehydrogenase. Choi IY, et al. Redox Rep, 2003. PMID 12631445
    4. Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP. Doyle SA, et al. Biochemistry, 2001 Apr 10. PMID 11284679
    5. From a dimer to a monomer: Construction of a chimeric monomeric isocitrate dehydrogenase. Tian C, et al. Protein Sci, 2021 Dec. PMID 34647384, Free PMC Article

    See all (81) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. From a dimer to a monomer: Construction of a chimeric monomeric isocitrate dehydrogenase.
      Title: From a dimer to a monomer: Construction of a chimeric monomeric isocitrate dehydrogenase.
    2. GltA, icd and mdh do not form a transcription unit, are scattered around the chromosome and are expressed from different promoters.
      Title: Interaction of enzymes of the tricarboxylic acid cycle in Bacillus subtilis and Escherichia coli: a comparative study.
    3. introduced single point mutations (Arg153His, Arg153Cys); both the R153H and R153C mutants nearly lost wild-type IDH activity yet acquired the neomorphic ability to catalyze the conversion of alpha-ketoglutarate to 2-hydroxyglutarate
      Title: Point mutation (R153H or R153C) in Escherichia coli isocitrate dehydrogenase: Biochemical characterization and functional implication.
    4. Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli
      Title: Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli.
    5. N-terminus verified by Edman degradation on complete protein
      Title: Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
    6. control of catalytic activity by phosphorylation [review]
      Title: Control of isocitrate dehydrogenase catalytic activity by protein phosphorylation in Escherichia coli.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables NAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables guanosine tetraphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables isocitrate dehydrogenase (NADP+) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables isocitrate dehydrogenase (NADP+) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within electron transport chain IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in glyoxylate cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within response to oxidative stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within tricarboxylic acid cycle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tricarboxylic acid cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    isocitrate dehydrogenase
    NP_415654.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      1195123..1196373
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_415654.1 isocitrate dehydrogenase [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_415654.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A5B9AN17, A0A5D8MS09, A0A8H9XRX7, A0A8S7JXI6
      Conserved Domains (1) summary
      PRK07006
      Location:8 → 416
      PRK07006; isocitrate dehydrogenase; Reviewed
    Nucleotide Protein
    Heading Accession and Version

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