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UniProtKB/Swiss-Prot entry P16100

[Entry info] [Name and origin] [References] [Comments] [Cross-references] [Keywords] [Features] [Sequence] [Tools]

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Entry information
Entry name IDH_AZOVI
Primary accession number P16100
Secondary accession numbers None
Integrated into Swiss-Prot on April 1, 1990
Sequence was last modified on January 23, 2007 (Sequence version 5)
Annotations were last modified on    November 25, 2008 (Entry version 72)
Name and origin of the protein
Protein name Isocitrate dehydrogenase [NADP]
Synonyms IDH
EC 1.1.1.42
Oxalosuccinate decarboxylase
Gene name
Name: icd
From
Azotobacter vinelandii [TaxID: 354] 
Taxonomy Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Azotobacter.
Protein existence 1: Evidence at protein level;
References
[1]
 NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-16.
DOI=10.1271/bbb.66.489; PubMed=12005040 [NCBI, ExPASy, EBI, Israel, Japan]
Sahara T., Takada Y., Takeuchi Y., Yamaoka N., Fukunaga N.;
"Cloning, sequencing, and expression of a gene encoding the monomeric isocitrate dehydrogenase of the nitrogen-fixing bacterium, Azotobacter vinelandii.";
Biosci. Biotechnol. Biochem. 66:489-500(2002).
[2]
 PRELIMINARY PROTEIN SEQUENCE OF 229-251 AND 255-260.
DOI=10.1021/bi00701a007; PubMed=4149369 [NCBI, ExPASy, EBI, Israel, Japan]
Edwards D.J., Heinrikson R.L., Chung A.E.;
"Triphosphopyridine nucleotide specific isocitrate dehydrogenase from Azotobacter vinelandii. Alkylation of a specific methionine residue and amino acid sequence of the peptide containing this residue.";
Biochemistry 13:677-683(1974).
[3]
 X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF COMPLEXES WITH ISOCITRATE; MANGANESE AND NADP, AND SUBUNIT.
DOI=10.1016/S0969-2126(02)00904-8; PubMed=12467571 [NCBI, ExPASy, EBI, Israel, Japan]
Yasutake Y., Watanabe S., Yao M., Takada Y., Fukunaga N., Tanaka I.;
"Structure of the monomeric isocitrate dehydrogenase: evidence of a protein monomerization by a domain duplication.";
Structure 10:1637-1648(2002).
Comments
  • CATALYTIC ACTIVITY: Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.
  • CATALYTIC ACTIVITY: Oxalosuccinate + 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).
  • BIOPHYSICOCHEMICAL PROPERTIES:
    Temperature dependence:   Optimum temperature is above 40 degrees Celsius;
  • SUBUNIT: Monomer.
  • 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.
  • SIMILARITY: Belongs to the monomeric-type IDH family.
Copyright
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms. Distributed under the Creative Commons Attribution-NoDerivs License.
Cross-references
Sequence databases
EMBL
D73443; BAA11169.1; -; Genomic_DNA.[EMBL / GenBank / DDBJ] [CoDingSequence]
PIR A10759; A10759.
JC7822; JC7822.
3D structure databases
PDB
1ITW; X-ray; 1.95 A; A/B/C/D=1-741.[ExPASy / RCSB / EBI]
1J1W; X-ray; 3.20 A; A/B/C/D=1-741.[ExPASy / RCSB / EBI]
Detailed list of linked structures.
PDBsum 1ITW; -.
1J1W; -.
ModBase P16100.
Enzyme and pathway databases
BioCyc MetaCyc:MON-13167; -.
Ontologies
GO
GO:0005737; Cellular component: cytoplasm (inferred from electronic annotation from UniProtKB-KW).
GO:0004450; Molecular function: isocitrate dehydrogenase (NADP+) activity (inferred from electronic annotation from InterPro).
GO:0000287; Molecular function: magnesium ion binding (inferred from electronic annotation from UniProtKB-KW).
GO:0030145; Molecular function: manganese ion binding (inferred from electronic annotation from UniProtKB-KW).
GO:0006097; Biological process: glyoxylate cycle (inferred from electronic annotation from UniProtKB-KW).
GO:0055114; Biological process: oxidation reduction (inferred from electronic annotation from UniProtKB-KW).
GO:0006099; Biological process: tricarboxylic acid cycle (inferred from electronic annotation from InterPro).
QuickGo view.
Family and domain databases
InterPro IPR004436; IsoCit_DHase_NAD_mono.
Graphical view of domain structure.
Pfam PF03971; IDH; 1.
Pfam graphical view of domain structure.
PIRSF PIRSF009407; IDH_monmr; 1.
TIGRFAMs TIGR00178; monomer_idh; 1.
ProtoNet P16100.
Other
UniRef View cluster of proteins with at least 50% / 90% / 100% identity.
Keywords
3D-structure; Cytoplasm; Direct protein sequencing; Glyoxylate bypass; Magnesium; Manganese; Metal-binding; NADP; Oxidoreductase; Phosphoprotein; Tricarboxylic acid cycle.
Features
SEVIEWER logo Feature table viewer FT aligner logo Feature aligner
KeyFrom   To Length Description FTId
INIT_MET   1     1        Removed. 
CHAIN   2   741  740     Isocitrate dehydrogenase [NADP]. PRO_0000083593
NP_BIND   82    87  6     NADP. 
NP_BIND   584   585  2     NADP. 
NP_BIND   600   602  3     NADP. 
REGION   132   139  8     Substrate binding. 
METAL   350   350        Magnesium or manganese. 
METAL   548   548        Magnesium or manganese. 
BINDING   135   135        NADP. 
BINDING   145   145        Substrate. 
BINDING   547   547        Substrate. 
BINDING   589   589        NADP. 
BINDING   649   649        NADP. 
SITE   255   255  1     Critical for catalysis (By similarity). 
SITE   420   420  1     Critical for catalysis (By similarity). 
STRAND   5    10  6      
HELIX   13    31  19      
TURN   32    34  3      
STRAND   36    41  6      
HELIX   44    51  8      
HELIX   53    55  3      
TURN   58    60  3      
HELIX   65    72  8      
STRAND   79    82  4      
HELIX   90   102  13      
HELIX   117   129  13      
STRAND   130   132  3      
HELIX   135   138  4      
STRAND   143   146  4      
HELIX   149   157  9      
STRAND   172   174  3      
STRAND   177   180  4      
HELIX   181   184  4      
STRAND   186   189  4      
STRAND   192   202  11      
STRAND   207   216  10      
STRAND   221   227  7      
HELIX   229   246  18      
STRAND   249   252  4      
TURN   256   258  3      
HELIX   262   274  13      
HELIX   276   281  6      
HELIX   283   288  6      
HELIX   293   295  3      
HELIX   297   303  7      
HELIX   304   306  3      
HELIX   309   325  17      
STRAND   331   333  3      
TURN   334   337  4      
STRAND   346   348  3      
HELIX   349   358  10      
TURN   359   361  3      
STRAND   362   364  3      
STRAND   368   376  9      
HELIX   380   396  17      
TURN   401   403  3      
STRAND   409   411  3      
TURN   414   416  3      
HELIX   418   421  4      
HELIX   423   425  3      
STRAND   426   428  3      
STRAND   430   439  10      
STRAND   444   450  7      
STRAND   455   461  7      
HELIX   463   480  18      
STRAND   484   487  4      
HELIX   493   506  14      
STRAND   516   519  4      
HELIX   521   533  13      
STRAND   539   542  4      
HELIX   544   559  16      
STRAND   562   571  10      
STRAND   576   580  5      
HELIX   587   596  10      
HELIX   604   620  17      
HELIX   624   642  19      
STRAND   649   653  5      
HELIX   656   673  18      
HELIX   678   693  16      
HELIX   695   703  9      
STRAND   715   717  3      
HELIX   720   727  8      
HELIX   731   736  6      
TURN   737   739  3      
Sequence information
Length: 741 AA [This is the length of the unprocessed precursor] Molecular weight: 80390 Da [This is the MW of the unprocessed precursor] CRC64: 29FF35278E5AED8B [This is a checksum on the sequence] 
        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
P16100 in FASTA format

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