The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans

Background: Isocitrate lyase catalyses the first committed step of the carb on-conserving glyoxylate bypass, the Mg2+-dependent reversible cleavage of isocitrate into succinate and glyoxylate. This metabolic pathway is an invi ting target for the control of a number of diseases, because the enzymes in volved in this cycle have been identified in many pathogens including Mycob acterium leprae and Leishmania. Results: As part of a programme of rational drug design the structure of th e tetrameric Aspergillus nidulans isocitrate lyase and its complex with gly oxylate and a divalent cation have been solved to 2.8 Angstrom resolution u sing X-ray diffraction. Each subunit comprises two domains, one of which ad opts a folding pattern highly reminiscent of the triose phosphate isomerase (TIM) barrel. A 'knot' between subunits observed in the three-dimensional structure, involving residues towards the C terminus, implies that tetramer assembly involves considerable flexibility in this part of the protein, Conclusions: Difference Fourier analysis together with the pattern of seque nce conservation has led to the identification of both the glyoxylate and m etal binding sites and implicates the C-terminal end of the TIM barrel as t he active site, which is consistent with studies of other enzymes with this fold. Two disordered regions of the polypeptide chain lie close to the act ive site, one of which includes a critical cysteine residue suggesting that conformational rearrangements are essential for catalysis. Structural simi larities between isocitrate lyase and both PEP mutase and enzymes belonging to the enolase superfamily suggest possible relationships in aspects of th e mechanism.