Molecular mechanisms of isocitrate dehydrogenase 1 (IDH1) mutations identified in tumors: The role of size and hydrophobicity at residue 132 on catalytic efficiency.
Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate (ICT) to α-ketoglutarate (αKG) in the cytosol and peroxisomes. Mutations in IDH1 have been implicated in >80% of lower grade gliomas and secondary glioblastomas and primarily affect residue 132, which helps coordinate substrate binding. However, other mutations found in the active site have also been identified in tumors. IDH1 mutations typically result in a loss of catalytic activity, but many also can catalyze a new reaction, the NADPH-dependent reduction of αKG to d-2-hydroxyglutarate (D2HG). D2HG is a proposed oncometabolite that can competitively inhibit αKG-dependent enzymes. Some kinetic parameters have been reported for several IDH1 mutations, and there is evidence that mutant IDH1 enzymes vary widely in their ability to produce D2HG. We report that most IDH1 mutations identified in tumors are severely deficient in catalyzing the normal oxidation reaction, but that D2HG production efficiency varies among mutant enzymes up to ∼640-fold. Common IDH1 mutations have moderate catalytic efficiencies for D2HG production, whereas rarer mutations exhibit either very low or very high efficiencies. We then designed a series of experimental IDH1 mutants to understand the features that support D2HG production. We show that this new catalytic activity observed in tumors is supported by mutations at residue 132 that have a smaller van der Waals volume and are more hydrophobic. We report that one mutation can support both the normal and neomorphic reactions. These studies illuminate catalytic features of mutations found in the majority of patients with lower grade gliomas.
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and.
Diego
D
Avellaneda Matteo
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and.
Adam J
AJ
Grunseth
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and.
Eric R
ER
Gonzalez
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and.
Stacy L
SL
Anselmo
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and.
Madison A
MA
Kennedy
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and.
Precious
P
Moman
the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037.
David A
DA
Scott
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and.
An
A
Hoang
From the Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182 and csohl@mail.sdsu.edu.
Christal D
CD
Sohl
D002384:Catalysis; D020134:Catalytic Domain; D002942:Circular Dichroism; D004305:Dose-Response Relationship, Drug; D008401:Gas Chromatography-Mass Spectrometry; D005910:Glioma / Q000378:metabolism; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D007521:Isocitrate Dehydrogenase / Q000737:chemistry / Q000235:genetics*; D009154:Mutation; D009249:NADP / Q000737:chemistry; D009369:Neoplasms / Q000201:enzymology / Q000235:genetics*; D010100:Oxygen / Q000737:chemistry; D015202:Protein Engineering; D055503:Protein Multimerization; D012984:Software; D013696:Temperature
D009249:NADP; D007521:Isocitrate Dehydrogenase; C543588:IDH1 protein, human; D010100:Oxygen
brain tumor; enzyme kinetics; enzyme mechanism; enzyme mutation; tumor metabolism