The 2-oxoglutarate dehydrogenase complex (OGDHC) is a key regulator of a branch point in the tricarboxylic acid cycle. It belongs to the family of 2-oxo acid dehydrogenase complexes which comprise multiple copies of the three catalytic enzyme components: E1, thiamine diphosphate (ThDP)-dependent 2-oxo acid dehydrogenase (in OGDHC it is E1o); E2, dihydrolipoyl acyltransferase with the covalently bound lipoic acid 2-Oxoglutarate dehydrogenase (OGDH) is the first and rate-limiting component of the multienzyme OGDH complex (OGDHC) whose malfunction is associated with neurodegeneration. The essential role of this complex in the degradation of glucose and glutamate, which have specific significance in brain, raises questions about the existence of brain-specific OGDHC isoenzyme(s). We purified OGDHC from extracts of brain or heart mitochondria using the same procedure of poly(ethylene glycol) fractionation, followed by size-exclusion chromatography. Chromatographic behavior and the insufficiency of mitochondrial disruption to solubilize OGDHC revealed functionally significant binding of the complex to membrane. Components of OGDHC from brain and heart were identified using nanohigh performance liquid chromatography electrospray tandem mass spectrometry after trypsinolysis of the electrophoretically separated proteins. In contrast to the heart complex, where only the known OGDH was determined, the band corresponding to the brain OGDH component was found to also include the novel 2-oxoglutarate dehydrogenase-like (OGDHL) protein. The ratio of identified peptides characteristic of OGDH and OGDHL was preserved during purification and indicated comparable quantities of the two proteins in brain. Brain OGDHC also differed from the heart complex in the abundance of the components, lower apparent molecular mass and decreased stability upon size-exclusion chromatography. The functional competence of the novel brain isoenzyme and different regulation of OGDH and OGDHL by 2-oxoglutarate are inferred from the biphasic dependence of the overall reaction rate versus 2-oxoglutarate concentration. OGDHL may thus participate in brain-specific control of 2-oxoglutarate distribution between energy production and synthesis of the neurotransmitter glutamate.Abbreviations E1, 2-oxo acid dehydrogenase; E2, dihydrolipoyl acyl transferase; E3, dihydrolipoyl dehydrogenase; nanoLC-MS ⁄ MS, nano-high performance liquid chromatography-electrospray tandem mass spectrometry; OGDH (E1o), 2-oxoglutarate dehydrogenase; OGDHC, 2-oxoglutarate dehydrogenase complex; OGDHL, 2-oxoglutarate dehydrogenase-like protein; ROS, reactive oxygen species; ThDP, thiamin diphosphate.