7UTC

Crystal structure of secondary alcohol dehydrogenases from the Thermoanaerobacter ethanolicus with NADP and transition-state analogue inhibitor DMSO

Replaces:  7JNQ

Summary for 7UTC

• Entry DOI: 10.2210/pdb7utc/pdb
• Descriptor: Secondary-alcohol dehydrogenase, ZINC ION, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (5 entities in total)
• Functional Keywords: secondary alcohol dehydrogenases, transition-state analogue inhibitor, dmso, nadp, oxidoreductase
• Biological source: Thermoanaerobacter pseudethanolicus
• Total number of polymer chains: 4
• Total formula weight: 156621.15

Authors

Dinh, T.,Phillips, R. (deposition date: 2022-04-26, release date: 2022-05-04, Last modification date: 2023-10-18)

Primary citation

Dinh, T.,Rahn, K.T.,Phillips, R.S.
Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from Thermoanaerobacter pseudoethanolicus reveal the dynamics of ligand exchange and the proton relay network.
Proteins, 90:1570-1583, 2022

PubMed Abstract: Three-dimensional structures of I86A and C295A mutant secondary alcohol dehydrogenase (SADH) from Thermoanaerobacter pseudoethanolicus were determined by x-ray crystallography. The tetrameric structure of C295A-SADH soaked with NADP and dimethyl sulfoxide (DMSO) was determined to 1.85 Å with an R of 0.225. DMSO is bound to the tetrahedral zinc in each subunit, with ligands from SG of Cys-37, NE2 of His-59, and OD2 of Asp-150. The nicotinamide ring of NADP is hydrogen-bonded to the N of Ala-295 and the O of Val-265 and Gly-293. The O of DMSO is connected to a network of hydrogen bonds with OG of Ser-39, the 3'-OH of NADP, and ND1 of His-42. The structure of I86A-SADH soaked with 2-pentanol and NADP contains (R)-2-pentanol bound in each subunit, ligated to the tetrahedral zinc, and connected to the proton relay network. The structure of I86A-SADH soaked with 3-methylcyclohexanol and NADP has alcohol bound in three subunits. Two of the sites have the alcohol ligated to the zinc in an axial position, with OE2 of Glu-60 in the other axial position of a trigonal bipyramidal complex. One site has 3-methylcyclohexanol bound noncovalently, with the zinc in an inverted tetrahedral geometry with Glu-60. The fourth site also has the zinc in a trigonal bipyramidal complex with axial Glu-60 and water ligands. These structures demonstrate that ligand exchange of SADH involves pentacoordinate and inverted zinc complexes with Glu-60. Furthermore, we see a network of hydrogen bonds connecting the substrate oxygen to the external solvent that is likely to play a role in the mechanism of SADH.

PubMed: 35357038
DOI: 10.1002/prot.26339

Experimental method

X-RAY DIFFRACTION (1.85 Å)