Escherichia coli K-12 substr. MG1655 Enzyme: isocitrate dehydrogenase

Gene: icd Accession Numbers: EG10489 (EcoCyc), b1136, ECK1122

Synonyms: icdE, icdA

Regulation Summary Diagram: ?

Regulation summary diagram for icd

Subunit composition of isocitrate dehydrogenase = [Icd]2

Alternative forms of isocitrate dehydrogenase: isocitrate dehydrogenase-P

Isocitrate dehydrogenase is the first bacterial enzyme shown to be regulated by phosphorylation/dephosphorylation. The modulation of this key enzyme activity enables E. coli to make rapid shifts between TCA and glyoxalate bypass pathways. Fluxes and intercellular concentrations for this junction have been determined. The state of phosphorylation of isocitrate dehydrogenase determines its activity. [Walsh85a, McKee89, LaPorte84]

There are marked differences in the properties of enzymes from different sources. The E. coli enzyme is not an allosteric protein as isocitrate dehydrogenases from other sources are, and it is cold sensitive. IcdA is observed to have several distinct isoforms [Link97]. Phosphorylation of the enzyme on a serine residue by isocitrate dehydrogenase kinase/phosphatase inactivates it, and dephosphorylation by the phosphatase reactivates it [Borthwick84, McKee89, Hurley89]. Phosphorylation affects the binding of NADP. This is the first bacterial enzyme shown to be regulated by phosphorylation/dephosphosphorylation [Borthwick84]. The 3D structure of the enzyme has been elucidated [Hurley89].

The enzyme shows allosteric inhibition by phosphoenolpyruvate [Ogawa07].

In some E. coli K-12 strains a defective prophage, e14, may be present. When present, it maps at the icd site and supplies the C terminal sequence of the gene, coding for 52 amino acid residues. Of the codon differences, most are synonymous, one is conservative. The properties of the enzyme seem not to be affected. [Hill89]

icd shows differential codon adaptation, resulting in differential translation efficiency signatures, in aerotolerant compared to obligate anaerobic microbes. It was therefore predicted to play a role in the oxidative stress response. An icd deletion mutant was shown to be more sensitive than wild-type specifically to hydrogen peroxide exposure, but not other stresses [Kri14].

Citations: [Thorsness87, Burke74, Burke73, Apostolakos82]

Gene Citations: [Prost99, Herold90]

Locations: cytosol

Map Position: [1,194,346 -> 1,195,596] (25.74 centisomes, 93°)
Length: 1251 bp / 416 aa

Molecular Weight of Polypeptide: 45.757 kD (from nucleotide sequence)

pI: 5.35

Unification Links: ASAP:ABE-0003823 , CGSC:615 , DIP:DIP-10006N , EchoBASE:EB0484 , EcoGene:EG10489 , EcoliWiki:b1136 , EcoO157Cyc:ICDA , ModBase:P08200 , OU-Microarray:b1136 , PortEco:icd , PR:PRO_000022989 , Pride:P08200 , Protein Model Portal:P08200 , RefSeq:NP_415654 , RegulonDB:EG10489 , SMR:P08200 , String:511145.b1136 , UniProt:P08200

Relationship Links: InterPro:IN-FAMILY:IPR001804 , InterPro:IN-FAMILY:IPR004439 , InterPro:IN-FAMILY:IPR019818 , InterPro:IN-FAMILY:IPR024084 , Panther:IN-FAMILY:PTHR11835 , PDB:Structure:1AI2 , PDB:Structure:1AI3 , PDB:Structure:1BL5 , PDB:Structure:1CW1 , PDB:Structure:1CW4 , PDB:Structure:1CW7 , PDB:Structure:1GRO , PDB:Structure:1GRP , PDB:Structure:1HJ6 , PDB:Structure:1IDC , PDB:Structure:1IDD , PDB:Structure:1IDE , PDB:Structure:1IDF , PDB:Structure:1IKA , PDB:Structure:1ISO , PDB:Structure:1P8F , PDB:Structure:1PB1 , PDB:Structure:1PB3 , PDB:Structure:1SJS , PDB:Structure:3ICD , PDB:Structure:3LCB , PDB:Structure:4AJ3 , PDB:Structure:4AJA , PDB:Structure:4AJB , PDB:Structure:4AJC , PDB:Structure:4AJR , PDB:Structure:4AJS , PDB:Structure:4BNP , PDB:Structure:4ICD , PDB:Structure:4P69 , PDB:Structure:5ICD , PDB:Structure:6ICD , PDB:Structure:7ICD , PDB:Structure:8ICD , PDB:Structure:9ICD , Pfam:IN-FAMILY:PF00180 , Prosite:IN-FAMILY:PS00470

In Paralogous Gene Group: 28 (3 members)

Reactions known to produce the compound:

Not in pathways:
a phosphorylated isocitrate dehydrogenase + H2O → an isocitrate dehydrogenase + phosphate

Reactions known to both consume and produce the compound:

Not in pathways:
an isocitrate dehydrogenase + ATP ↔ ADP + a phosphorylated isocitrate dehydrogenase

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for icd

GO Terms:

Biological Process: GO:0006979 - response to oxidative stress Inferred from experiment [Kri14]
GO:0022900 - electron transport chain Inferred from experiment [Lakshmi76, Kabir04]
GO:0006097 - glyoxylate cycle Inferred by computational analysis [UniProtGOA11a]
GO:0006099 - tricarboxylic acid cycle Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0004450 - isocitrate dehydrogenase (NADP+) activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Thorsness87, Zhang11]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051287 - NAD binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Garnak79]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism energy metabolism, carbon TCA cycle

Essentiality data for icd knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 3]

Enzymatic reaction of: isocitrate dehydrogenase

Synonyms: oxalosuccinate decarboxylase, isocitrate dehydrogenase (NADP+)

EC Number:

D-threo-isocitrate + NADP+ <=> 2-oxoglutarate + CO2 + NADPH

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass , superpathway of glyoxylate bypass and TCA , TCA cycle I (prokaryotic) , mixed acid fermentation

Citations: [Nimmo84]

Cofactors or Prosthetic Groups: Mn2+

Alternative Cofactors for Mn2+: Mg2+ [Comment 4 ]

Inhibitors (Allosteric): phosphoenolpyruvate [Ogawa07]

Inhibitors (Competitive): 3-oxalomalate , glyoxylate [Comment 5] , oxaloacetate [Comment 5]

Inhibitors (Unknown Mechanism): phenylglyoxal [Comment 6]

T(opt): 50 °C [BRENDA14, Stokke07]

Sequence Features

Protein sequence of Icd with features indicated

Feature Class Location Attached Group Citations Comment
Mutagenesis-Variant 100  
[Zhang11, UniProt12a]
K → E or R: Abolishes enzymatic activity.
N6-succinyllysine-Modification 100  
[Zhang11, UniProt12a]
UniProt: N6-succinyllysine.
Amino-Acid-Sites-That-Bind 104  
[Doyle01, Hurley89, Bolduc95, UniProt15]
UniProt: NADP.
Mutagenesis-Variant 113  
[Hurley90, UniProt11]
S → D or E: Reduced affinity for isocitrate.
Phosphorylation-Modification 113  
[Hurley90, UniProt11]
UniProt: Phosphoserine.
Amino-Acid-Sites-That-Bind 113  
[Thorsness87, UniProt11]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 115  
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 119  
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 129  
UniProt: Substrate.
N6-acetyllysine-Modification 142  
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Amino-Acid-Sites-That-Bind 153  
UniProt: Substrate.
Amino-Acid-Site 160  
UniProt: Critical for catalysis; Sequence Annotation Type: site.
Mutagenesis-Variant 160  
[Bolduc95, Lee95, UniProt11]
UniProt: Large decrease in activity and a small increase in substrate affinity.
Acetylation-Modification 177  
Amino-Acid-Site 230  
UniProt: Critical for catalysis; Sequence Annotation Type: site.
Mutagenesis-Variant 230  
[Bolduc95, Lee95, UniProt11]
UniProt: Decrease in activity and substrate affinity.
Acetylation-Modification 235  
Mutagenesis-Variant 242  
[Zhang11, UniProt12a]
[Zhang11, UniProt12a]
K → R: Impairs enzymatic activity.
K → E: Strongly impairs enzymatic activity.
N6-succinyllysine-Modification 242  
[Zhang11, UniProt12a]
UniProt: N6-succinyllysine.
Acetylation-Modification 242  
Acetylation-Modification 265  
Metal-Binding-Site 307  
[Doyle01, Bolduc95, Hurley90, UniProt15]
UniProt: Magnesium or manganese.
Nucleotide-Phosphate-Binding-Region 339 -> 345 NADP+
[Doyle01, Hurley89, Bolduc95, UniProt15]
UniProt: NADP.
Amino-Acid-Sites-That-Bind 352  
[Doyle01, Hurley89, Bolduc95, UniProt15]
UniProt: NADP; via amide nitrogen and carbonyl oxygen.
Acetylation-Modification 378  
Amino-Acid-Sites-That-Bind 391  
[Doyle01, Hurley89, Bolduc95, UniProt15]
UniProt: NADP.
Amino-Acid-Sites-That-Bind 395  
[Doyle01, Hurley89, Bolduc95, UniProt15]
UniProt: NADP.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1136 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10489; confirmed by SwissProt match.


Apostolakos82: Apostolakos D, Menter PA, Rampsch BJ, Reeves HC, Birge EA "Genetic map position of the cistron coding for isocitrate dehydrogenase in Escherichia coli K-12." Current Microbiology 1982;7:45-47.

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bolduc95: Bolduc JM, Dyer DH, Scott WG, Singer P, Sweet RM, Koshland DE, Stoddard BL (1995). "Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase." Science 268(5215);1312-8. PMID: 7761851

Borthwick84: Borthwick AC, Holms WH, Nimmo HG (1984). "The phosphorylation of Escherichia coli isocitrate dehydrogenase in intact cells." Biochem J 1984;222(3);797-804. PMID: 6385963

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Burke73: Burke WF, Swafford JR, Reeves HC (1973). "Crystallization of NADP-specific isocitrate dehydrogenase." Science 1973;181(94);59-60. PMID: 4145959

Burke74: Burke WF, Johanson RA, Reeves HC (1974). "NADP+-specific isocitrate dehydrogenase of Escherichia coli. II. Subunit structure." Biochim Biophys Acta 1974;351(2);333-40. PMID: 4152156

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Doyle01: Doyle SA, Beernink PT, Koshland DE (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(14);4234-41. PMID: 11284679

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Garnak79: Garnak M, Reeves HC (1979). "Phosphorylation of Isocitrate dehydrogenase of Escherichia coli." Science 203(4385);1111-2. PMID: 34215

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Herold90: Herold C, Birge EA (1990). "Location of icdA and fadR on the physical map of Escherichia coli." J Bacteriol 1990;172(12);6618. PMID: 2254241

Hill89: Hill CW, Gray JA, Brody H (1989). "Use of the isocitrate dehydrogenase structural gene for attachment of e14 in Escherichia coli K-12." J Bacteriol 1989;171(7);4083-4. PMID: 2661545

Hurley89: Hurley JH, Thorsness PE, Ramalingam V, Helmers NH, Koshland DE, Stroud RM (1989). "Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase." Proc Natl Acad Sci U S A 1989;86(22);8635-9. PMID: 2682654

Hurley90: Hurley JH, Dean AM, Sohl JL, Koshland DE, Stroud RM (1990). "Regulation of an enzyme by phosphorylation at the active site." Science 249(4972);1012-6. PMID: 2204109

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kabir04: Kabir MM, Shimizu K (2004). "Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements." Appl Microbiol Biotechnol 65(1);84-96. PMID: 15221231

Kri14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

Lakshmi76: Lakshmi TM, Helling RB (1976). "Selection for citrate synthase deficiency in icd mutants of Escherichia coli." J Bacteriol 127(1);76-83. PMID: 776950

LaPorte84: LaPorte DC, Walsh K, Koshland DE (1984). "The branch point effect. Ultrasensitivity and subsensitivity to metabolic control." J Biol Chem 1984;259(22);14068-75. PMID: 6389540

Lee95: Lee ME, Dyer DH, Klein OD, Bolduc JM, Stoddard BL, Koshland DE (1995). "Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli." Biochemistry 34(1);378-84. PMID: 7819221

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

McKee89: McKee JS, Nimmo HG (1989). "Evidence for an arginine residue at the coenzyme-binding site of Escherichia coli isocitrate dehydrogenase." Biochem J 1989;261(1);301-4. PMID: 2673216

Nimmo84: Nimmo GA, Nimmo HG (1984). "The regulatory properties of isocitrate dehydrogenase kinase and isocitrate dehydrogenase phosphatase from Escherichia coli ML308 and the roles of these activities in the control of isocitrate dehydrogenase." Eur J Biochem 1984;141(2);409-14. PMID: 6329757

Nimmo86: Nimmo HG (1986). "Kinetic mechanism of Escherichia coli isocitrate dehydrogenase and its inhibition by glyoxylate and oxaloacetate." Biochem J 1986;234(2);317-23. PMID: 3521584

Ogawa07: Ogawa T, Murakami K, Mori H, Ishii N, Tomita M, Yoshin M (2007). "Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coli." J Bacteriol 189(3);1176-8. PMID: 17142397

Prost99: Prost JF, Negre D, Oudot C, Murakami K, Ishihama A, Cozzone AJ, Cortay JC (1999). "Cra-dependent transcriptional activation of the icd gene of Escherichia coli." J Bacteriol 1999;181(3);893-8. PMID: 9922253

Reeves72: Reeves HC, Daumy GO, Lin CC, Houston M (1972). "NADP + -specific isocitrate dehydrogenase of Escherichia coli. I. Purification and characterization." Biochim Biophys Acta 1972;258(1);27-39. PMID: 4400493

Stokke07: Stokke R, Karlstrom M, Yang N, Leiros I, Ladenstein R, Birkeland NK, Steen IH (2007). "Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers." Extremophiles 11(3);481-93. PMID: 17401542

Thorsness87: Thorsness PE, Koshland DE (1987). "Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate." J Biol Chem 1987;262(22);10422-5. PMID: 3112144

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Walsh85a: Walsh K, Koshland DE (1985). "Branch point control by the phosphorylation state of isocitrate dehydrogenase. A quantitative examination of fluxes during a regulatory transition." J Biol Chem 1985;260(14);8430-7. PMID: 2861202

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Zhang11: Zhang Z, Tan M, Xie Z, Dai L, Chen Y, Zhao Y (2011). "Identification of lysine succinylation as a new post-translational modification." Nat Chem Biol 7(1);58-63. PMID: 21151122

Other References Related to Gene Regulation

Chao97: Chao G, Shen J, Tseng CP, Park SJ, Gunsalus RP (1997). "Aerobic regulation of isocitrate dehydrogenase gene (icd) expression in Escherichia coli by the arcA and fnr gene products." J Bacteriol 1997;179(13);4299-304. PMID: 9209047

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Park14: Park DM, Kiley PJ (2014). "The influence of repressor DNA binding site architecture on transcriptional control." MBio 5(5). PMID: 25161193

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038

ShalelLevanon05: Shalel-Levanon S, San KY, Bennett GN (2005). "Effect of oxygen, and ArcA and FNR regulators on the expression of genes related to the electron transfer chain and the TCA cycle in Escherichia coli." Metab Eng 7(5-6):364-74. PMID: 16140031

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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