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P16100 (IDH_AZOVI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Isocitrate dehydrogenase [NADP]
Short name=IDH
EC=1.1.1.42
Alternative name(s):
Oxalosuccinate decarboxylase
Gene names
Name:icd
OrganismAzotobacter vinelandii
Taxonomic identifier354 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Azotobacter

Protein attributes

Sequence length741 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

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

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

Subunit structure

Monomer. Ref.3

Subcellular location

Cytoplasm.

Domain

This molecule consists of two distinct domains, a small domain and a large domain. The structure of the large domain repeats a motif observed in the dimeric IDH. Such a fusional structure by domain duplication enables a single polypeptide chain to form a structure at the catalytic site that is homologous to the dimeric IDH, the catalytic site of which is located at the interface of two identical subunits.

Sequence similarities

Belongs to the monomeric-type IDH family.

Biophysicochemical properties

Temperature dependence:

Optimum temperature is above 40 degrees Celsius.

Ontologies

Keywords
   Biological processGlyoxylate bypass
Tricarboxylic acid cycle
   Cellular componentCytoplasm
   LigandMagnesium
Manganese
Metal-binding
NADP
   Molecular functionOxidoreductase
   PTMPhosphoprotein
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processglyoxylate cycle

Inferred from electronic annotation. Source: UniProtKB-KW

tricarboxylic acid cycle

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionisocitrate dehydrogenase (NADP+) activity

Inferred from electronic annotation. Source: EC

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.1
Chain2 – 741740Isocitrate dehydrogenase [NADP]
PRO_0000083593

Regions

Nucleotide binding82 – 876NADP
Nucleotide binding584 – 5852NADP
Nucleotide binding600 – 6023NADP
Region132 – 1398Substrate binding

Sites

Metal binding3501Magnesium or manganese
Metal binding5481Magnesium or manganese
Metal binding5521Magnesium or manganese By similarity
Binding site1351NADP
Binding site1451Substrate
Binding site5471Substrate
Binding site5891NADP
Binding site6491NADP
Site2551Critical for catalysis By similarity
Site4201Critical for catalysis By similarity

Secondary structure

1 ..................................................................................................................................... 741
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P16100 [UniParc].

Last modified January 23, 2007. Version 5.
Checksum: 29FF35278E5AED8B

FASTA74180,390
        10         20         30         40         50         60 
MSTPKIIYTL TDEAPALATY SLLPIIKAFT GSSGIAVETR DISLAGRLIA TFPEYLTDTQ 

        70         80         90        100        110        120 
KISDDLAELG KLATTPDANI IKLPNISASV PQLKAAIKEL QQQGYKLPDY PEEPKTDTEK 

       130        140        150        160        170        180 
DVKARYDKIK GSAVNPVLRE GNSDRRAPLS VKNYARKHPH KMGAWSADSK SHVAHMDNGD 

       190        200        210        220        230        240 
FYGSEKAALI GAPGSVKIEL IAKDGSSTVL KAKTSVQAGE IIDSSVMSKN ALRNFIAAEI 

       250        260        270        280        290        300 
EDAKKQGVLL SVHLKATMMK VSDPIMFGQI VSEFYKDALT KHAEVLKQIG FDVNNGIGDL 

       310        320        330        340        350        360 
YARIKTLPEA KQKEIEADIQ AVYAQRPQLA MVNSDKGITN LHVPSDVIVD ASMPAMIRDS 

       370        380        390        400        410        420 
GKMWGPDGKL HDTKAVIPDR CYAGVYQVVI EDCKQHGAFD PTTMGSVPNV GLMAQKAEEY 

       430        440        450        460        470        480 
GSHDKTFQIP ADGVVRVTDE SGKLLLEQSV EAGDIWRMCQ AKDAPIQDWV KLAVNRARAT 

       490        500        510        520        530        540 
NTPAVFWLDP ARAHDAQVIA KVERYLKDYD TSGLDIRILS PVEATRFSLA RIREGKDTIS 

       550        560        570        580        590        600 
VTGNVLRDYL TDLFPIMELG TSAKMLSIVP LMSGGGLFET GAGGSAPKHV QQFLEEGYLR 

       610        620        630        640        650        660 
WDSLGEFLAL AASLEHLGNA YKNPKALVLA STLDQATGKI LDNNKSPARK VGEIDNRGSH 

       670        680        690        700        710        720 
FYLALYWAQA LAAQTEDKEL QAQFTGIAKA LTDNETKIVG ELAAAQGKPV DIAGYYHPNT 

       730        740 
DLTSKAIRPS ATFNAALAPL A

« Hide

References

[1]"Cloning, sequencing, and expression of a gene encoding the monomeric isocitrate dehydrogenase of the nitrogen-fixing bacterium, Azotobacter vinelandii."
Sahara T., Takada Y., Takeuchi Y., Yamaoka N., Fukunaga N.
Biosci. Biotechnol. Biochem. 66:489-500(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-16.
[2]"Triphosphopyridine nucleotide specific isocitrate dehydrogenase from Azotobacter vinelandii. Alkylation of a specific methionine residue and amino acid sequence of the peptide containing this residue."
Edwards D.J., Heinrikson R.L., Chung A.E.
Biochemistry 13:677-683(1974) [PubMed] [Europe PMC] [Abstract]
Cited for: PRELIMINARY PROTEIN SEQUENCE OF 229-251 AND 255-260.
[3]"Structure of the monomeric isocitrate dehydrogenase: evidence of a protein monomerization by a domain duplication."
Yasutake Y., Watanabe S., Yao M., Takada Y., Fukunaga N., Tanaka I.
Structure 10:1637-1648(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF COMPLEXES WITH ISOCITRATE; MANGANESE AND NADP, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		D73443 Genomic DNA. Translation: BAA11169.1.
PIRA10759.
JC7822.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ITWX-ray1.95A/B/C/D1-741[»]
1J1WX-ray3.20A/B/C/D1-741[»]
ProteinModelPortalP16100.
SMRP16100. Positions 2-741.
ModBaseSearch...

Proteomic databases

PRIDEP16100.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-13167.

Family and domain databases

Gene3D3.40.718.10. 3 hits.
InterProIPR004436. Isocitrate_DH_NADP_mono.
IPR024084. IsoPropMal-DH-like_dom.
[Graphical view]
PfamPF03971. IDH. 1 hit.
[Graphical view]
PIRSFPIRSF009407. IDH_monmr. 1 hit.
TIGRFAMsTIGR00178. monomer_idh. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP16100.

Entry information

Entry nameIDH_AZOVI
AccessionPrimary (citable) accession number: P16100
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: January 23, 2007
Last modified: April 3, 2013
This is version 95 of the entry and version 5 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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