4F7I

Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in complex with IPM, Mn and NADH

Summary for 4F7I

• Entry DOI: 10.2210/pdb4f7i/pdb
• Related: 1HEX 2Y3Z 2Y40 2Y41 2Y42 2ZTW
• Descriptor: 3-isopropylmalate dehydrogenase, 3-ISOPROPYLMALIC ACID, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (9 entities in total)
• Functional Keywords: isopropylmalate dehydrogenase, 3-ipm-dh, beta-ipm dehydrogenase, imdh, ipmdh, oxidoreductase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 4
• Total formula weight: 161022.26

Authors

Pallo, A.,Graczer, E.,Zavodszky, P.,Weiss, M.S.,Vas, M. (deposition date: 2012-05-16, release date: 2012-06-13, Last modification date: 2023-09-13)

Primary citation

Pallo, A.,Olah, J.,Graczer, E.,Merli, A.,Zavodszky, P.,Weiss, M.S.,Vas, M.
Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis.
Febs J., 281:5063-5076, 2014

PubMed Abstract: The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn(2+) , its substrate isopropylmalate and its co-factor product NADH at 2.0 Å resolution features a fully closed conformation of the enzyme. Upon closure of the two domains, the substrate and the co-factor are brought into precise relative orientation and close proximity, with a distance between the C2 atom of the substrate and the C4N atom of the pyridine ring of the co-factor of approximately 3.0 Å. The structure further shows binding of a K(+) ion close to the active site, and provides an explanation for its known activating effect. Hence, this structure is an excellent mimic for the enzymatically competent complex. Using high-level QM/MM calculations, it may be demonstrated that, in the observed arrangement of the reactants, transfer of a hydride from the C2 atom of 3-isopropylmalate to the C4N atom of the pyridine ring of NAD(+) is easily possible, with an activation energy of approximately 15 kcal·mol(-1) . The activation energy increases by approximately 4-6 kcal·mol(-1) when the K(+) ion is omitted from the calculations. In the most plausible scenario, prior to hydride transfer the ε-amino group of Lys185 acts as a general base in the reaction, aiding the deprotonation reaction of 3-isopropylmalate prior to hydride transfer by employing a low-barrier proton shuttle mechanism involving a water molecule.

PubMed: 25211160
DOI: 10.1111/febs.13044

Experimental method

X-RAY DIFFRACTION (2 Å)