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

Gene ID: 945702, updated on 2-May-2024

Summary

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Gene symbol
icd
Gene description
isocitrate dehydrogenase
Primary source
ASAP:ABE-0003823
Locus tag
b1136
See related
ECOCYC:EG10489
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. 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
  2. Point mutation (R153H or R153C) in Escherichia coli isocitrate dehydrogenase: Biochemical characterization and functional implication. Song P, et al. J Basic Microbiol, 2017 Jan. PMID 27406240
  3. Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli. Dexter JP, et al. J Biol Chem, 2013 Feb 22. PMID 23192354, Free PMC Article
  4. Identification of lysine succinylation as a new post-translational modification. Zhang Z, et al. Nat Chem Biol, 2011 Jan. PMID 21151122, Free PMC Article
  5. An SOD mimic protects NADP+-dependent isocitrate dehydrogenase against oxidative inactivation. Batinic-Haberle I, et al. Free Radic Res, 2008 Jul. PMID 18608518, 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
    A0A7D7DVA6
    Conserved Domains (1) summary
    PRK07006
    Location:8 → 416
    PRK07006; isocitrate dehydrogenase; Reviewed
Nucleotide Protein
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Gene LinkOut

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Other Literature Sources
Molecular Biology Databases