Iso_dhIsocitrate/isopropylmalate dehydrogenase |
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SMART accession number: | SM01329 |
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Description: | Isocitrate dehydrogenase (IDH), is an important enzyme of carbohydrate metabolism which catalyses the oxidative decarboxylation of isocitrate into alpha-ketoglutarate. |
Interpro abstract (IPR024084): | This entry represents a structural domain found in all types of isocitrate dehydrogenase, and in isopropylmalate dehydrogenase and tartrate dehydrogenase. The crystal structure of Escherichia coli isopropylmalate dehydrogenase has been described [ (PUBMED:9086278) ]. The isocitrate and isopropylmalate dehydrogenases family includes isocitrate dehydrogenase (IDH), 3-isopropylmalate dehydrogenase (IMDH) and tartrate dehydrogenase. IDH is an important enzyme of carbohydrate metabolism which catalyses the oxidative decarboxylation of isocitrate into alpha-ketoglutarate [ (PUBMED:2682654) (PUBMED:1939242) ]. IDH is either dependent on NAD + ( EC 1.1.1.41 ) or on NADP + ( EC 1.1.1.42 ). In eukaryotes there are at least three isozymes of IDH: two are located in the mitochondrial matrix (one NAD + -dependent, the other NADP + -dependent), while the third one (also NADP + -dependent) is cytoplasmic. In Escherichia coli, the activity of a NADP + -dependent form of the enzyme is controlled by the phosphorylation of a serine residue; the phosphorylated form of IDH is completely inactivated. IMDH ( EC 1.1.1.85 ) catalyses the third step in the biosynthesis of leucine in bacteria and fungi, the oxidative decarboxylation of 3-isopropylmalate into 2-oxo-4-methylvalerate [ (PUBMED:1748999) (PUBMED:7773180) ]. Tartrate dehydrogenase ( EC 1.1.1.93 ) shows strong homology to prokaryotic isopropylmalate dehydrogenases and, to a lesser extent, isocitrate dehydrogenase [ (PUBMED:8053675) ]. It catalyses the reduction of tartrate to oxaloglycolate [ (PUBMED:8053675) ]. |
GO process: | oxidation-reduction process (GO:0055114) |
GO function: | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616) |
Family alignment: |
There are 52899 Iso_dh domains in 52895 proteins in SMART's nrdb database.
Click on the following links for more information.
- Evolution (species in which this domain is found)
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Taxonomic distribution of proteins containing Iso_dh domain.
This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Iso_dh domain is also avaliable.
Click on the protein counts, or double click on taxonomic names to display all proteins containing Iso_dh domain in the selected taxonomic class.
- Cellular role (predicted cellular role)
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Cellular role: metabolism
- Literature (relevant references for this domain)
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Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Cupp JR, McAlister-Henn L
- NAD(+)-dependent isocitrate dehydrogenase. Cloning, nucleotide sequence, anddisruption of the IDH2 gene from Saccharomyces cerevisiae.
- J Biol Chem. 1991; 266: 22199-205
- Display abstract
NAD(+)-dependent isocitrate dehydrogenase from Saccharomyces cerevisiae iscomposed of two nonidentical subunits, designated IDH1 (Mr approximately 40,000) and IDH2 (Mr approximately 39,000). We have isolated and characterized a yeastgenomic clone containing the IDH2 gene. The amino acid sequence deduced from the gene indicates that IDH2 is synthesized as a precursor of 369 amino acids (Mr39,694) and is processed upon mitochondrial import to yield a mature protein of354 amino acids (Mr 37,755). Amino acid sequence comparison between S. cerevisiaeIDH2 and S. cerevisiae NADP(+)-dependent isocitrate dehydrogenase shows nosignificant sequence identity, whereas comparison of IDH2 and Escherichia coliNADP(+)-dependent isocitrate dehydrogenase reveals a 33% sequence identity. Toconfirm the identity of the IDH2 gene and examine the relationship between IDH1and IDH2, the IDH2 gene was disrupted by genomic replacement in a haploid yeaststrain. The disruption strain expressed no detectable IDH2, as determined byWestern blot analysis, and was found to lack NAD(+)-dependent isocitratedehydrogenase activity, indicating that IDH2 is essential for a functionalenzyme. Overexpression of IDH2, however, did not result in increasedNAD(+)-dependent isocitrate dehydrogenase activity, suggesting that both IDH1 andIDH2 subunits are required for catalytic activity. The disruption strain wasunable to utilize acetate as a carbon source and exhibited a 2-fold slower growthrate than wild type strains on glycerol or lactate. This growth phenotype isconsistent with NAD(+)-dependent isocitrate dehydrogenase performing an essentialrole in the oxidative function of the citric acid cycle.
- Hurley JH, Thorsness PE, Ramalingam V, Helmers NH, Koshland DE Jr, Stroud RM
- Structure of a bacterial enzyme regulated by phosphorylation, isocitratedehydrogenase.
- Proc Natl Acad Sci U S A. 1989; 86: 8635-9
- Display abstract
The structure of isocitrate dehydrogenase [threo-DS-isocitrate: NADP+oxidoreductase (decarboxylating), EC 1.1.1.42] from Escherichia coli has beensolved and refined at 2.5 A resolution and is topologically different from thatof any other dehydrogenase. This enzyme, a dimer of identical 416-residuesubunits, is inactivated by phosphorylation at Ser-113, which lies at the edge ofan interdomain pocket that also contains many residues conserved betweenisocitrate dehydrogenase and isopropylmalate dehydrogenase. Isocitratedehydrogenase contains an unusual clasp-like domain in which both polypeptidechains in the dimer interlock. Based on the structure of isocitrate dehydrogenaseand conservation with isopropylmalate dehydrogenase, we suggest that the activesite lies in an interdomain pocket close to the phosphorylation site.
- Structure (3D structures containing this domain)
3D Structures of Iso_dh domains in PDB
PDB code Main view Title 1a05 CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE 1ai2 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CALCIUM (FLASH-COOLED) 1ai3 ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES 1bl5 ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION 1cm7 3-ISOPROPYLMALATE DEHYDROGENASE FROM ESCHERICHIA COLI 1cnz 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) FROM SALMONELLA TYPHIMURIUM 1cw1 CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE MUTANT K230M BOUND TO ISOCITRATE AND MN2+ 1cw4 CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATE 1cw7 LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-ISOCITRATE 1dpz STUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD711 1dr0 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD708 1dr8 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD177 1g2u THE STRUCTURE OF THE MUTANT, A172V, OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 : ITS THERMOSTABILITY AND STRUCTURE. 1gc8 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TO PHE 1gc9 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TO GLY 1gro REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115 1grp REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115 1hex STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH NAD+: LIGAND-INDUCED LOOP-CLOSING AND MECHANISM FOR COFACTOR SPECIFICITY 1hj6 ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED) 1hqs CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE FROM BACILLUS SUBTILIS 1idc ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY 1idd ISOCITRATE DEHYDROGENASE Y160F MUTANT APO ENZYME 1ide ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE COMPLEX (LAUE DETERMINATION) 1idf ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME 1idm 3-ISOPROPYLMALATE DEHYDROGENASE, LOOP-DELETED CHIMERA 1ika STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE 1ipd THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-ISOPROPYLMALATE DEHYDROGENASE OF THERMUS THERMOPHILUS AT 2.2 ANGSTROMS RESOLUTION 1iso ISOCITRATE DEHYDROGENASE: STRUCTURE OF AN ENGINEERED NADP+--> NAD+ SPECIFICITY-REVERSAL MUTANT 1lwd CRYSTAL STRUCTURE OF NADP-DEPENDENT ISOCITRATE DEHYDROGENASE FROM PORCINE HEART MITOCHONDRIA 1osi STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE 1osj STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE 1p8f A four location model to explain the stereospecificity of proteins. 1pb1 A four location model to explain the stereospecificity of proteins. 1pb3 Sites of binding and orientation in a four location model for protein stereospecificity. 1sjs ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY DOMAIN SHIFTING 1t09 Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex NADP 1t0l Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+) 1tyo Isocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix in complex with etheno-NADP 1v53 The crystal structure of 3-isopropylmalate dehydrogenase from Bacillus coagulans 1v5b The Structure Of The Mutant, S225A and E251L, Of 3-Isopropylmalate Dehydrogenase From Bacillus Coagulans 1v94 Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix 1vlc Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution 1w0d The high resolution structure of Mycobacterium tuberculosis LeuB (Rv2995c) 1wal 3-ISOPROPYLMALATE DEHYDROGENASE (IPMDH) MUTANT (M219A)FROM THERMUS THERMOPHILUS 1wpw Crystal Structure of IPMDH from Sulfolobus tokodaii 1x0l Crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, Thermus thermophilus 1xaa 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE 1xab 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (150K) STRUCTURE 1xac CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (100K) STRUCTURE. 1xad CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (150K) STRUCTURE. 1xgv Isocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix 1xkd Ternary complex of Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix 1zor Isocitrate dehydrogenase from the hyperthermophile Thermotoga maritima 2ayq 3-ISOPROPYLMALATE DEHYDROGENASE FROM THE MODERATE FACULTATIVE THERMOPHILE, BACILLUS COAGULANS 2cmj Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase 2cmv Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase complexed with Cadmium and citrate 2d1c Crystal Structure Of TT0538 protein from Thermus thermophilus HB8 2d4v Crystal structure of NAD dependent isocitrate dehydrogenase from Acidithiobacillus thiooxidans 2dht Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7 2e0c crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7 at 2.0 A resolution 2e5m Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain 7 2g4o anomalous substructure of 3-ISOPROPYLMALATE DEHYDROGENASE 2iv0 Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers. 2qfv Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with NADP(+) 2qfw Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with isocitrate 2qfx Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with NADPH, a-ketoglutarate and Ca(2+) 2qfy Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with a-ketoglutarate 2uxq Isocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila: biochemical properties and crystal structure analysis 2uxr Complex with isocitrate and the protein isocitrate dehydrogenase from the psychrophilic bacterium Desulfotalea psychrophila 2y3z Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - apo enzyme 2y40 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with Mn 2y41 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with IPM and MN 2y42 Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH and Mn 2ztw Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ 3ah3 Crystal structure of LR5-1, 3-isopropylmalate dehydrogenase created by directed evolution 3asj Crystal structure of homoisocitrate dehydrogenase in complex with a designed inhibitor 3blv Yeast Isocitrate Dehydrogenase with Citrate Bound in the Regulatory Subunits 3blw Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits 3blx Yeast Isocitrate Dehydrogenase (Apo Form) 3dms 1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei 3flk Crystal Structure of Tartrate Dehydrogenase from Pseudomonas putida in complex with NADH, oxalate and metal ion 3fmx Crystal structure of Tartrate dehydrogenase from Pseudomonas putida complexed with NADH 3icd STRUCTURE OF A BACTERIAL ENZYME REGULATED BY PHOSPHORYLATION, ISOCITRATE DEHYDROGENASE 3inm Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+) 3lcb The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli. 3map Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate 3mar Crystal structure of homodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP 3mas Crystal structure of heterodimeric R132H mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate 3r8w Structure of 3-isopropylmalate dehydrogenase isoform 2 from Arabidopsis thaliana at 2.2 angstrom resolution 3ty3 Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe bound to glycyl-glycyl-glycine 3ty4 Crystal structure of homoisocitrate dehydrogenase from Schizosaccharomyces pombe 3u1h Crystal structure of IPMDH from the last common ancestor of Bacillus 3udo Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni 3udu Crystal structure of putative 3-isopropylmalate dehydrogenase from Campylobacter jejuni 3us8 Crystal Structure of an isocitrate dehydrogenase from Sinorhizobium meliloti 1021 3vkz 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at atmospheric pressure 3vl2 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 160 MPa 3vl3 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 340 MPa 3vl4 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 410 MPa 3vl6 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 580 MPa 3vl7 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 650 MPa 3vmj 3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 3vmk 3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2 3vml Chimera 3-isopropylmalate dehydrogenase between Shewanella oneidensis MR-1 (O) and Shewanella benthica DB21 MT-2 (M) from N-terminal: 20% O middle 70% M residual 10% O 3wzv 3WZV 3wzw 3WZW 3wzx 3WZX 3wzy 3WZY 4aj3 3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex 4aja 3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and thioNADP 4ajb 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with Isocitrate, calcium(II) and thioNADP 4ajc 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, calcium(II) and adenine nucleotide phosphate 4ajr 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with alpha-ketoglutarate, magnesium(II) and NADPH - The product complex 4ajs 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate 4aou CtIDH bound to NADP. The complex structures of Isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila, support a new active site locking mechanism 4aov DpIDH-NADP. The complex structures of Isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila, support a new active site locking mechanism 4aoy Open CtIDH. The complex structures of Isocitrate dehydrogenase from Clostridium thermocellum and Desulfotalea psychrophila, support a new active site locking mechanism 4bnp 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate and magnesium(II) 4f7i Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH 4hcx Structure of ICDH-1 from M.tuberculosis complexed with NADPH & Mn2+ 4i3k Crystal structure of a metabolic reductase with 1-hydroxy-6-(4-hydroxybenzyl)-4-methylpyridin-2(1H)-one 4i3l Crystal structure of a metabolic reductase with 6-benzyl-1-hydroxy-4-methylpyridin-2(1H)-one 4icd REGULATION OF ISOCITRATE DEHYDROGENASE BY PHOSPHORYLATION INVOLVES NO LONG-RANGE CONFORMATIONAL CHANGE IN THE FREE ENZYME 4iwh Crystal structure of a 3-isopropylmalate dehydrogenase from Burkholderia pseudomallei 4ja8 Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with AGI-6780 Inhibitor 4kzo Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate 4l03 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate 4l04 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate 4l06 Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate 4p69 4P69 4umx 4UMX 4umy 4UMY 4wuo 4WUO 4xrx 4XRX 4xs3 4XS3 4xxv 4XXV 4y1p 4Y1P 4yb4 4YB4 5de1 5DE1 5icd REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE 5j32 5J32 5j33 5J33 5j34 5J34 5k10 5K10 5k11 5K11 6icd REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE 7icd REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE 8icd REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE 9icd CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES - Links (links to other resources describing this domain)
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PFAM Iso_dh INTERPRO IPR024084