Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P08200 (IDH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 141. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Isocitrate dehydrogenase [NADP]

Short name=IDH
EC=1.1.1.42
Alternative name(s):
IDP
NADP(+)-specific ICDH
Oxalosuccinate decarboxylase
Gene names
Name:icd
Synonyms:icdA, icdE
Ordered Locus Names:b1136, JW1122
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length416 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH. Ref.10

Cofactor

Binds 1 magnesium or manganese ion per subunit.

Enzyme regulation

Inhibition of this enzyme by phosphorylation regulates the branch point between the Krebs cycle and the glyoxylate bypass, which is an alternate route that accumulates carbon for biosynthesis when acetate is the sole carbon source for growth.

Subunit structure

Homodimer. Ref.13

Post-translational modification

Phosphorylation state of this enzyme is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK).

Succinylation probably inhibits enzymatic activity. Ref.10

Sequence similarities

Belongs to the isocitrate and isopropylmalate dehydrogenases family.

Biophysicochemical properties

Kinetic parameters:

KM=11.4 µM for isocitrate Ref.7 Ref.12

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 416416Isocitrate dehydrogenase [NADP]
PRO_0000083551

Regions

Nucleotide binding339 – 3457NADP

Sites

Metal binding3071Magnesium or manganese
Binding site1041NADP
Binding site1131Substrate Ref.1
Binding site1151Substrate
Binding site1191Substrate
Binding site1291Substrate
Binding site1531Substrate
Binding site3521NADP; via amide nitrogen and carbonyl oxygen
Binding site3911NADP
Binding site3951NADP
Site1601Critical for catalysis
Site2301Critical for catalysis

Amino acid modifications

Modified residue1001N6-succinyllysine Ref.10
Modified residue1131Phosphoserine Ref.11
Modified residue1421N6-acetyllysine Ref.9
Modified residue2421N6-succinyllysine Ref.10

Experimental info

Mutagenesis1001K → R or E: Abolishes enzymatic activity. Ref.10
Mutagenesis1131S → D or E: Reduced affinity for isocitrate. Ref.11
Mutagenesis1601Y → F: Large decrease in activity and a small increase in substrate affinity. Ref.7 Ref.12
Mutagenesis2301K → M: Decrease in activity and substrate affinity. Ref.7 Ref.12
Mutagenesis2421K → E: Strongly impairs enzymatic activity. Ref.10
Mutagenesis2421K → R: Impairs enzymatic activity. Ref.10

Secondary structure

.................................................................................... 416
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P08200 [UniParc].

Last modified August 1, 1988. Version 1.
Checksum: 9A02E707C3B4FDD9

FASTA41645,757
        10         20         30         40         50         60 
MESKVVVPAQ GKKITLQNGK LNVPENPIIP YIEGDGIGVD VTPAMLKVVD AAVEKAYKGE 

        70         80         90        100        110        120 
RKISWMEIYT GEKSTQVYGQ DVWLPAETLD LIREYRVAIK GPLTTPVGGG IRSLNVALRQ 

       130        140        150        160        170        180 
ELDLYICLRP VRYYQGTPSP VKHPELTDMV IFRENSEDIY AGIEWKADSA DAEKVIKFLR 

       190        200        210        220        230        240 
EEMGVKKIRF PEHCGIGIKP CSEEGTKRLV RAAIEYAIAN DRDSVTLVHK GNIMKFTEGA 

       250        260        270        280        290        300 
FKDWGYQLAR EEFGGELIDG GPWLKVKNPN TGKEIVIKDV IADAFLQQIL LRPAEYDVIA 

       310        320        330        340        350        360 
CMNLNGDYIS DALAAQVGGI GIAPGANIGD ECALFEATHG TAPKYAGQDK VNPGSIILSA 

       370        380        390        400        410 
EMMLRHMGWT EAADLIVKGM EGAINAKTVT YDFERLMDGA KLLKCSEFGD AIIENM 

« Hide

References

« Hide 'large scale' references
[1]"Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate."
Thorsness P.E., Koshland D.E. Jr.
J. Biol. Chem. 262:10422-10425(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map."
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. expand/collapse author list , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T.
DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"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. 179:6551-6559(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 11-414.
Strain: CH734.
[6]"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
Link A.J., Robison K., Church G.M.
Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-12.
Strain: K12 / EMG2.
[7]"Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli."
Lee M.E., Dyer D.H., Klein O.D., Bolduc J.M., Stoddard B.L., Koshland D.E. Jr.
Biochemistry 34:378-384(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME KINETICS, MUTAGENESIS OF TYR-160 AND LYS-230.
[8]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[9]"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-142, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
[10]"Identification of lysine succinylation as a new post-translational modification."
Zhang Z., Tan M., Xie Z., Dai L., Chen Y., Zhao Y.
Nat. Chem. Biol. 7:58-63(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: CATALYTIC ACTIVITY, SUCCINYLATION AT LYS-100 AND LYS-242, MUTAGENESIS OF LYS-100 AND LYS-242.
Strain: K12.
[11]"Regulation of an enzyme by phosphorylation at the active site."
Hurley J.H., Dean A.M., Sohl J.L., Koshland D.E. Jr., Stroud R.M.
Science 249:1012-1016(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH ISOCITRATE AND MAGNESIUM, PHOSPHORYLATION AT SER-113, MUTAGENESIS OF SER-113.
[12]"Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase."
Bolduc J.M., Dyer D.H., Scott W.G., Singer P., Sweet R.M., Koshland D.E. Jr., Stoddard B.L.
Science 268:1312-1318(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH ISOCITRATE; NADP AND MAGNESIUM, MUTAGENESIS OF TYR-160 AND LYS-230, BIOPHYSICOCHEMICAL PROPERTIES.
[13]"Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase."
Hurley J.H., Thorsness P.E., Ramalingam V., Helmers N.H., Koshland D.E. Jr., Stroud R.M.
Proc. Natl. Acad. Sci. U.S.A. 86:8635-8639(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH NADP, SUBUNIT.
[14]"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. Jr.
J. Mol. Biol. 295:377-385(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF MUTANT MET-230.
[15]"Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP."
Doyle S.A., Beernink P.T., Koshland D.E. Jr.
Biochemistry 40:4234-4241(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT GLU-113 IN COMPLEX WITH SUBSTRATE ANALOG; MAGNESIUM AND NADP.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J02799 Genomic DNA. Translation: AAA24006.1.
U00096 Genomic DNA. Translation: AAC74220.1.
AP009048 Genomic DNA. Translation: BAA35958.1.
AF017587 Genomic DNA. Translation: AAC45887.1.
PIRDCECIS. A28482.
RefSeqNP_415654.1. NC_000913.3.
YP_489404.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AI2X-ray1.90A1-416[»]
1AI3X-ray1.90A1-416[»]
1BL5X-ray2.50A3-416[»]
1CW1X-ray2.10A1-416[»]
1CW4X-ray2.10A1-416[»]
1CW7X-ray2.60A1-416[»]
1GROX-ray2.50A1-416[»]
1GRPX-ray2.50A1-416[»]
1HJ6X-ray2.00A1-416[»]
1IDCX-ray2.50A1-416[»]
1IDDX-ray2.50A1-416[»]
1IDEX-ray2.50A1-416[»]
1IDFX-ray2.50A1-416[»]
1IKAX-ray2.70A1-416[»]
1ISOX-ray1.90A1-416[»]
1P8FX-ray1.85A1-416[»]
1PB1X-ray1.70A1-416[»]
1PB3X-ray1.70A1-416[»]
1SJSX-ray2.42A1-416[»]
3ICDX-ray2.50A1-416[»]
3LCBX-ray2.90C/D1-416[»]
4AJ3X-ray1.90A1-416[»]
4AJAX-ray1.80A1-416[»]
4AJBX-ray1.90A1-416[»]
4AJCX-ray2.30A1-416[»]
4AJRX-ray2.69A1-416[»]
4AJSX-ray1.80A1-416[»]
4ICDX-ray2.50A1-416[»]
5ICDX-ray2.50A1-416[»]
6ICDX-ray2.80A1-416[»]
7ICDX-ray2.40A1-416[»]
8ICDX-ray2.50A1-416[»]
9ICDX-ray2.50A1-416[»]
ProteinModelPortalP08200.
SMRP08200. Positions 1-416.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10006N.
IntActP08200. 6 interactions.
STRING511145.b1136.

PTM databases

PhosSiteP010427.

2D gel databases

SWISS-2DPAGEP08200.

Proteomic databases

PaxDbP08200.
PRIDEP08200.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74220; AAC74220; b1136.
BAA35958; BAA35958; BAA35958.
GeneID12934062.
945702.
KEGGecj:Y75_p1106.
eco:b1136.
PATRIC32117521. VBIEscCol129921_1183.

Organism-specific databases

EchoBASEEB0484.
EcoGeneEG10489. icd.
EG10009. icdC.

Phylogenomic databases

eggNOGCOG0538.
HOGENOMHOG000021113.
KOK00031.
OMAFRDWGYE.
OrthoDBEOG6SNDTP.
PhylomeDBP08200.
ProtClustDBPRK07006.

Enzyme and pathway databases

BioCycEcoCyc:ISOCITDEH-SUBUNIT.
ECOL316407:JW1122-MONOMER.
MetaCyc:ISOCITDEH-SUBUNIT.
SABIO-RKP08200.

Gene expression databases

GenevestigatorP08200.

Family and domain databases

Gene3D3.40.718.10. 1 hit.
InterProIPR019818. IsoCit/isopropylmalate_DH_CS.
IPR001804. Isocitrate/isopropylmalate_DH.
IPR004439. Isocitrate_DH_NADP_dimer_prok.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PANTHERPTHR11835. PTHR11835. 1 hit.
PfamPF00180. Iso_dh. 1 hit.
[Graphical view]
TIGRFAMsTIGR00183. prok_nadp_idh. 1 hit.
PROSITEPS00470. IDH_IMDH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP08200.
PROP08200.

Entry information

Entry nameIDH_ECOLI
AccessionPrimary (citable) accession number: P08200
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1988
Last modified: April 16, 2014
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene