5KJ1

G173A horse liver alcohol dehydrogenase complexed with NAD+ and pentafluorobenzyl alcohol

Summary for 5KJ1

• Entry DOI: 10.2210/pdb5kj1/pdb
• Related: 4DWV 5KCP 5KCZ 5KJ6 5KJC 5KJE 5KJF
• Descriptor: Alcohol dehydrogenase E chain, ZINC ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM), ... (6 entities in total)
• Functional Keywords: oxidoreductase inhibitor complex rossmann fold dynamics, oxidoreductase
• Biological source: Equus caballus (Horse)
• Total number of polymer chains: 2
• Total formula weight: 82191.96

Authors

Plapp, B.V. (deposition date: 2016-06-17, release date: 2016-07-06, Last modification date: 2023-10-18)

Primary citation

Plapp, B.V.,Gakhar, L.,Subramanian, R.
Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase.
Acta Crystallogr D Struct Biol, 78:1221-1234, 2022

PubMed Abstract: 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 Å 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 Å) 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 Å for the overall complexes and of 5-10 Å 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 ∼0.3 Å 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.

PubMed: 36189742
DOI: 10.1107/S2059798322008361

Experimental method

X-RAY DIFFRACTION (1.2 Å)