Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate.
The structure of the isocitrate dehydrogenase (IDH) complex with bound alpha-ketoglutarate, Ca2+, and NADPH was solved at 2.7-A resolution. The alpha-ketoglutarate binds in the active site at the same position and orientation as isocitrate, with a difference between the two bound molecules of about 0.8 A. The Ca2+ metal is coordinated by alpha-ketoglutarate, three conserved aspartate residues, and a pair of water molecules. The largest motion in the active site relative to the isocitrate enzyme complex is observed for tyrosine 160, which originally forms a hydrogen bond to the labile carboxyl group of isocitrate and moves to form a new hydrogen bond to Asp 307 in the complex with alpha-ketoglutarate. This triggers a number of significant movements among several short loops and adjoining secondary structural elements in the enzyme, most of which participate in dimer stabilization and formation of the active-site cleft. These rearrangements are similar to the ligand-binding-induced movements observed in globins and insulin and serve as a model for an enzymatic mechanism which involves local shifts of secondary structural elements during turnover, rather than large-scale domain closures or loop transitions induced by substrate binding such as those observed in hexokinase or triosephosphate isomerase.
Stoddard
B L
BL
Department of Molecular and Cellular Biology, University of California, Berkeley 94720.
Koshland
D E
DE
D001665:Binding Sites; D002118:Calcium / Q000737:chemistry; D007521:Isocitrate Dehydrogenase / Q000737:chemistry*; D007523:Isocitrates / Q000737:chemistry*; D007656:Ketoglutaric Acids / Q000737:chemistry*; D011487:Protein Conformation; D014961:X-Ray Diffraction
D007523:Isocitrates; D007656:Ketoglutaric Acids; C034219:isocitric acid; D007521:Isocitrate Dehydrogenase; D002118:Calcium