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Publication Abstract from PubMed

Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD(+) and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD(+) and 2,2,2-trifluoroethanol were determined to 1.1-1.3 A resolution below the ;glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 A(2)) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 A(2) for the overall complexes and of 5-10 A(2) for C4N of NAD(+) and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of approximately 0.3 A and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD(+) and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.

Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase.,Plapp BV, Gakhar L, Subramanian R Acta Crystallogr D Struct Biol. 2022 Oct 1;78(Pt 10):1221-1234. doi: , 10.1107/S2059798322008361. Epub 2022 Sep 27. PMID:36189742^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.