Well ordered crystals of a short-chain alcohol dehydrogenase from Drosophila lebanonensis: re-evaluation of the crystallographic data and rotation-function analysis

Abstract

Alcohol dehydrogenase prepared from Drosophila lebanonesis yields well ordered plate-like crystals which diffract to better than 2.3 A resolution. The crystals belong to space group P21 of the monoclinic system; the unit-cell dimensions are a = 65.25, b = 55.77, c = 70.02 A~, a = 90,/3 = 107.08, y = 90 ~. The asymmetric unit of the crystal cell is most probably occupied by a dimer, corresponding to a packing density of 2.15 ~3 Da-l. The orientation of the noncrystallographic twofold symmetry axes is determined by analysis of a self-rotation function calculated with native intensity data.

Drosophila alcohol dehydrogenase: evaluation of Ser139 site‐directed mutants

“…The structural information of the 138–158 fragment reported in this work was obtained from the refined X ray structure of DADH [3]and Benach et al (to be published). Ser 139 is located at the end of the strand βE, enclosed in the turn connecting βE and helix αF, Tyr 152 is at the N‐terminal end of the αF‐helix and Lys 156 is in the same α‐helix (Fig.…”

“…D. lebanonensis active site coordinates were from X‐ray analysis data [3]and a refined crystallographic model ( R =20.1%, R free =24.0%, resolution range=8–1.92 Å). Crystal structures were from the Brookhaven Protein Data Bank (PDB): 3α,20β‐HSDH (PDB code: 2HSD) [11, 12], DHPR (PDB code: 1DHR) [15, 21]and UDP (PDB code: 1UDP) [22].…”

“…DADH is a short‐chain dehydrogenase/reductase (SDR) [2], an extended protein family, whose members show highly diverse functions, structure, subunit number and tissue distribution. Many primary structures for DADH have been reported, 57 sequences belonging to 45 Drosophila species, and the refined 3D structure of DADH is soon available [3].…”

The catalytic reaction and inhibition mechanism of Drosophila alcohol dehydrogenase: observation of an enzyme-bound NAD-ketone adduct at 1.4 Å resolution by X-ray crystallography

“…Binary (enzyme Ácoenzyme) and ternary (enzyme Ácoenzyme Á inhibitor) complexes were prepared by co-crystallization. They were crystallized by the sitting drop vapor-diffusion method as published previously (Ladenstein et al, 1995). The coenzyme (10 mM NAD for the binary complex (BIN), 1 mM NAD for the ternary complexes) was dissolved in the protein solution and 1 % of ketone (acetone (ADA), 3-pentanone (ADO) or cyclohexanone (ADC)) was added to the reservoir solution before the droplets (5-10 ml) were set.…”

Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family

“…Dimerization of short- and medium-chain dehydrogenases is a prerequisite for their activity. ,,− Calculations of the crystallographic dimer with Proteins, Interfaces, Structures and Assemblies (PISA) indicated a biologic origin of the dimeric state (Table S3). Furthermore, evolutionary analysis of the protein–protein interface with Evolutionary Protein–protein Interface Classifier (EPPIC) supported data calculated by PISA that classified the interface as being of biological origin (Figure and Table S4).…”