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Catalytic Site Atlas

CSA LITERATURE entry for 1a05

E.C. name3-isopropylmalate dehydrogenase
SpeciesThiobacillus ferrooxidans (Acidithiobacillus ferrooxidans)
E.C. Number (IntEnz) 1.1.1.85
CSA Homologues of 1a05There are 84 Homologs
CSA Entries With UniProtID Q56268
CSA Entries With EC Number 1.1.1.85
PDBe Entry 1a05
PDBSum Entry 1a05
MACiE Entry 1a05

Literature Report

IntroductionIsocitrate dehydrogenase has long been known to be a key enzyme in the Krebs cycle, and isozymes are found in both the mitochondrial matrix and the cytosol of eukaryotes, and in bacteria. In addition to the usual NADP dependent form (EC 1.1.1.42), eukaryotes have an NAD dependent isozyme (EC 1.1.1.41). More recently, two other NAD dependent enzymes - isopropylmalate dehydrogenase (EC 1.1.1.85) and tartrate dehydrogenase (EC 1.1.1.93) have been recognised to be related by sequence and mechanism to isocitrate dehydrogenase - the unusual feature being that all of them decarboxylate the substrate which they oxidise. These are both found in micro-organisms and are involved in leucine biosynthesis and glyoxylate metabolism respectively. All require an Mg2+ ion for catalysis.
MechansimThe oxidation reaction is believed to occur in two steps - dehydrogenation at the alpha-carbon to form a carbonyl and decarboxylation at the beta-carbon. First, Asp B222 deprotonates the 2-hydroxy oxygen, followed by the formation of a double bond forcing hydride transfer from C2 to NAD(P). In the case of isocitrate dehydrogenase, the intermediate so formed is oxalosuccinate and is stable enough to be isolated. In vivo, however, the beta-carboxylate group is rapidly lost and C3 is stereospecifically protonated to form the product. Lys B190 is vital for the decarboxylation step in providing the proton, and the Tyr A140 hydroxyl is very important for the oxidation step in participating in hydride transfer. Magnesium stabilises the negative charge on the hydroxyl oxygen during the dehydrogenation and decarboxylation steps.
Reaction

Catalytic Sites for 1a05

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
TyrA140140macie:sideChainParticipates in hydride transfer from the substrate to NAD(P).
AspB222222macie:sideChainActs as a general base catalyst to deprotonate the hydroxyl oxygen of the substrate in the dehydrogenation step.
LysB190190macie:sideChainActs as a general acid catalyst in protonation in the decarboxylation step.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA222222macie:sideChainActs as a general base catalyst to deprotonate the hydroxyl oxygen of the substrate in the dehydrogenation step.
LysA190190macie:sideChainActs as a general acid catalyst in protonation in the decarboxylation step.
TyrB140140macie:sideChainParticipates in hydride transfer from the substrate to NAD(P).

Literature References

Notes:
Lee ME
Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP(+)-dependent isocitrate dehydrogenase from Escherichia coli.
Biochemistry 1995 34 378-384
PubMed: 7819221
Miyazaki K
Tyr-139 in Thermus thermophilus 3-isopropylmalate dehydrogenase is involved in catalytic function.
FEBS Lett 1993 332 37-38
PubMed: 8405446
Hurley JH
Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes.
Biochemistry 1991 30 8671-8678
PubMed: 1888729
Imada K
Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.
Structure 1998 6 971-982
PubMed: 9739088
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