Ligand-induced changes in the conformation of 3-isopropylmalate dehydrogenase from Thermus thermophilus.
The structures of 3-isopropylmalate dehydrogenase (IPMDH) from Thermus thermophilus in complexes with its substrate, cofactor, and a cofactor analog were investigated by X-ray diffraction in a crystalline state and by small-angle X-ray scattering (SAXS) in solution. The structures at 2.8 A resolution of the complexes with the substrate, 3-isopropylmalate (IPM), and with an analog of NAD, ADP-ribose, were both very close to the structure of the free enzyme, which adopts an open conformation. However, the binding of a ligand induced a small conformational change near the binding site. This result contrasts with results for NADP(+)-bound and isocitrate-bound isocitrate dehydrogenase (ICDH) from Escherichia coli, which adopts a closed conformation. The SAXS analysis in solution clearly showed that IPMDH without a ligand adopts two distinct intermediate conformations, between the open and closed states, upon binding of NADH and IPM respectively, and adopts a fully closed conformation when in a ternary complex with NADH and IPM together.
Kadono
S
S
Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama.
Sakurai
M
M
Moriyama
H
H
Sato
M
M
Hayashi
Y
Y
Oshima
T
T
Tanaka
N
N
D050539:3-Isopropylmalate Dehydrogenase; D000429:Alcohol Oxidoreductases / Q000378:metabolism*; D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008024:Ligands; D008969:Molecular Sequence Data; D011487:Protein Conformation / Q000187:drug effects; D016415:Sequence Alignment; D016963:Thermus thermophilus / Q000201:enzymology*
D008024:Ligands; D000429:Alcohol Oxidoreductases; D050539:3-Isopropylmalate Dehydrogenase