Journal article
Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase
Acta crystallographica. Section D, Structural biology, Vol.78(10), pp.1221-1234
10/01/2022
DOI: 10.1107/S2059798322008361
PMCID: PMC9527765
PMID: 36189742
Appears in UI Libraries Support Open Access
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 angstrom 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 angstrom(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 angstrom(2) for the overall complexes and of 5-10 angstrom(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 similar to 0.3 angstrom 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.
Details
- Title: Subtitle
- Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase
- Creators
- Bryce Plapp - Univ Iowa, Dept Biochem & Mol Biol, Iowa City, IA 52252 USALokesh Gakhar - Univ Iowa, Carver Coll Med, Prot & Crystallog Facil, Iowa City, IA 52252 USARamaswamy Subramanian - Univ Iowa, Dept Biochem & Mol Biol, Iowa City, IA 52252 USA
- Resource Type
- Journal article
- Publication Details
- Acta crystallographica. Section D, Structural biology, Vol.78(10), pp.1221-1234
- DOI
- 10.1107/S2059798322008361
- PMID
- 36189742
- PMCID
- PMC9527765
- NLM abbreviation
- Acta Crystallogr D Struct Biol
- ISSN
- 2059-7983
- eISSN
- 2059-7983
- Publisher
- Wiley
- Number of pages
- 14
- Grant note
- AA00279 / National Institute on Alcohol Abuse and Alcoholism; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Alcohol Abuse & Alcoholism (NIAAA) GM078446 / National Institute of General Medical Sciences; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) United States Public Health Service; United States Department of Health & Human Services
- Language
- English
- Date published
- 10/01/2022
- Academic Unit
- Biochemistry and Molecular Biology; Medicine Administration
- Record Identifier
- 9984323230502771
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