Fundamental molecular differences between alcohol dehydrogenase classes

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 06/1994; 91(11):4980-4. DOI: 10.1073/pnas.91.11.4980
Source: PubMed


Two types of alcohol dehydrogenase in separate protein families are the "medium-chain" zinc enzymes (including the classical liver and yeast forms) and the "short-chain" enzymes (including the insect form). Although the medium-chain family has been characterized in prokaryotes and many eukaryotes (fungi, plants, cephalopods, and vertebrates), insects have seemed to possess only the short-chain enzyme. We have now also characterized a medium-chain alcohol dehydrogenase in Drosophila. The enzyme is identical to insect octanol dehydrogenase. It is a typical class III alcohol dehydrogenase, similar to the corresponding human form (70% residue identity), with mostly the same residues involved in substrate and coenzyme interactions. Changes that do occur are conservative, but Phe-51 is of functional interest in relation to decreased coenzyme binding and increased overall activity. Extra residues versus the human enzyme near position 250 affect the coenzyme-binding domain. Enzymatic properties are similar--i.e., very low activity toward ethanol (Km beyond measurement) and high selectivity for formaldehyde/glutathione (S-hydroxymethylglutathione; kcat/Km = 160,000 min-1.mM-1). Between the present class III and the ethanol-active class I enzymes, however, patterns of variability differ greatly, highlighting fundamentally separate molecular properties of these two alcohol dehydrogenases, with class III resembling enzymes in general and class I showing high variation. The gene coding for the Drosophila class III enzyme produces an mRNA of about 1.36 kb that is present at all developmental stages of the fly, compatible with the constitutive nature of the vertebrate enzyme. Taken together, the results bridge a previously apparent gap in the distribution of medium-chain alcohol dehydrogenases and establish a strictly conserved class III enzyme, consistent with an important role for this enzyme in cellular metabolism.

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    • "EVOLUTION AND STRUCTURE OF ADH-P GENE FAMILIES It has been recognized for more than a decade that the ADH- P gene family originated from a glutathione-dependent formaldehyde dehydrogenase gene (GSH-FDH), also known as Class III ADH, sometime after the divergence of the plant and animal kingdoms (Figure 3). The argument rests on the presence of GSH-FDH genes in virtually all life forms, and the tight conservation of amino acid sequence (Danielsson et al., 1994): e.g. pea and human GSH-FDHs show 69% amino acid identity, compared with 47% between their respective ADHs, and there are just three changes in 23 amino acids deemed important for substrate and co-enzyme binding (Martínez et al., 1996; Shafqat et al., 1996). "
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    ABSTRACT: The structures, evolution and functions of alcohol dehydrogenase gene families and their products have been scrutinized for half a century. Our understanding of the enzyme structure and catalytic activity of plant alcohol dehydrogenase (ADH-P) is based on the vast amount of information available for its animal counterpart. The probable origins of the enzyme from a simple β-coil and eventual emergence from a glutathione-dependent formaldehyde dehydrogenase have been well described. There is compelling evidence that the small ADH gene families found in plants today are the survivors of multiple rounds of gene expansion and contraction. To the probable original function of their products in the terminal reaction of anaerobic fermentation have been added roles in yeast-like aerobic fermentation and the production of characteristic scents that act to attract animals that serve as pollinators or agents of seed dispersal and to protect against herbivores.
    Preview · Article · Apr 2011 · The Plant Journal
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    • "The presence of Adh3 enzymes in all animals so far investigated and the evolutionary constancy of Adh3 (Danielsson et al., 1994) argue in favor of an ancient and essential physiological role for Adh3 enzymes in distantly related animals. For instance, Adh3 might be involved in regulating formaldehyde levels (Koivusalo et al., 1989), which is potentially connected to the essential serine-and folate-dependent one-carbon metabolism that occurs in digestive tissues and is required for development (Thompson et al., 2001). "
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    ABSTRACT: Enzymes that synthesize retinoic acid (RA) constitute the first level of regulation of RA action. In vertebrates, enzymes of the medium-chain alcohol dehydrogenase (MDR-Adh) family catalyze the first step of the RA synthetic pathway by oxidizing retinol. Among MDR-Adh enzymes, Adh3 is the only member present in non-vertebrates, and whether Adh3 is actually involved in RA biosynthesis remains uncertain. Here, we investigate the MDR-Adh family in Oikopleura dioica, a urochordate representing the sister group to vertebrates. Oikopleura is of special interest because it has lost the classical RA role in development, which relaxed evolutionary constraints to preserve the RA-genetic machinery, leading to the loss of RA-system components. The hypothesis that Adh3 plays a role in RA synthesis predicts that the relaxation of selection in Oikopleura should have led to the loss of Adh3, or changes in residues related to retinol oxidation. The hypothesis also predicts changes in the expression pattern of Oikopleura Adh3 compared to other chordates that preserved RA-signaling. Our results, however, revealed the presence of a highly conserved Adh3 gene in Oikopleura, with no significant changes in functional residues. Our results also revealed that the Oikopleura Adh3 expression remains unchanged in comparison to other non-vertebrate chordates, restricted to specific compartments of the digestive system. Because Adh3 has been highly conserved in an animal that has dismantled the RA system, we conclude that Adh3 preservation is not due to a conserved role in RA synthesis. Thereby, if Adh3 plays a role in RA synthesis in vertebrates, it might be a lineage-specific neofunctionalization.
    Full-text · Article · Feb 2010 · ZOOLOGICAL SCIENCE
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    • " segments ( V1 , V2 and V3 ) can also be distinguished , that are responsible for the enzyme ' s hypervariability . They corre - spond to a portion ( V1 , residues 49 – 61 ) adjacent to the active site ; a loop near the zinc atom ( V2 , residues 100 – 130 ) ; and a region of monomer interaction ( V3 , residues 290 – 310 ) ( Person et al . , 1993 ; Danielsson et al . , 1994 ) . The Adh copies may have been retained as a consequence of adaptative amino acid replacements which have conferred subtle changes in function . Slightly different constraints on the protein sequence may lead to subsequent differences in non - synonymous substitution rates between gene copies , as found by Gaut et al . ( 1999 ) . Desp"
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    ABSTRACT: The glycolytic proteins in plants are coded by small multigene families, which provide an interesting contrast to the high copy number of gene families studied to date. The alcohol dehydrogenase (Adh) genes encode glycolytic enzymes that have been characterized in some plant families. Although the amino acid sequences of zinc-containing long-chain ADHs are highly conserved, the metabolic function of this enzyme is variable. They also have different patterns of expression and are submitted to differences in nonsynonymous substitution rates between gene copies. It is possible that the Adh copies have been retained as a consequence of adaptative amino acid replacements which have conferred subtle changes in function. Phylogenetic analysis indicates that there have been a number of separate duplication events within angiosperms, and that genes labeled Adh1, Adh2 and Adh3 in different groups may not be homologous. Nonsynonymous/synonymous ratios yielded no signs of positive selection. However, the coefficients of functional divergence (theta) estimated between the Adh1 and Adh2 gene groups indicate statistically significant site-specific shift of evolutionary rates between them, as well as between those of different botanical families, suggesting that altered functional constraints may have taken place at some amino acid residues after their diversification. The theoretical three-dimensional structure of the alcohol dehydrogenase from Arabis blepharophylla was constructed and verified to be stereochemically valid.
    Full-text · Article · Aug 2007 · Gene
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