Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes

Abstract

Short-chain dehydrogenases/reductases (SDRs) constitute a large family of NAD(P)(H)-dependent oxidoreductases, sharing sequence motifs and displaying similar mechanisms. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, cofactor, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. Sequence identities are low, and the most conserved feature is an alpha/beta folding pattern with a central beta sheet flanked by 2 - 3 alpha-helices from each side, thus a classical Rossmannfold motif for nucleotide binding. The conservation of this element and an active site, often with an Asn-Ser-Tyr-Lys tetrad, provides a platform for enzymatic activities encompassing several EC classes, including oxidoreductases, epimerases and lyases. The common mechanism is an underlying hydride and proton transfer involving the nicotinamide and typically an active site tyrosine residue, whereas substrate specificity is determined by a variable C-terminal segment. Relationships exist with bacterial haloalcohol dehalogenases, which lack cofactor binding but have the active site architecture, emphasizing the versatility of the basic fold in also generating hydride transfer-independent lyases. The conserved fold and nucleotide binding emphasize the role of SDRs as scaffolds for an NAD(P)(H) redox sensor system, of importance to control metabolic routes, transcription and signalling.

Figure 1

Ribbon diagram comparison of classical SDR, extended SDR, MDR and LDR enzymes. The Rossmann-fold motif is depicted with beta strands in blue and helices in red; additional domains and secondary structural elements are shown in grey. The nucleotide cofactor is drawn in ball-and-stick representation. (A) Classical SDR (3α/20β HSD; PDB 2hsd). (B) Extended SDR (galactose epimerase; PDB 1xel). (C) MDR (horse liver ADH; PDB 1hld). (D) LDR (mannitol DH; PDB 1m2w).

Figure 2

Reactions catalyzed by SDR enzymes.

Figure 3

Proton relay in ‘classical’ SDRs [45]. Shown is the active site architecture of bacterial 3β/17β-hydroxysteroid dehydrogenase (PDB id 1hxh), with NAD+ (lower left) and a modelled 3β-hydroxysteroid (upper left corner). Hydride transfer is to the 4-pro- S of the nicotinamide (left blue arrow), whereas a proton path is generated through side chains of the active site tyrosine, lysine, the nicotinamide ribose hydroxyl and a conserved water molecule, which is stabilized by the main-chain carbonyl of a conserved asparaginyl residue.

Figure 4

Active site features of the ‘divergent’ SDR dienoyl-CoA reductase (1w6u). Active site residues are shown with yellow carbons and labelled, while the active site residues of the classical SDR 3α/20β-HSD are superimposed in grey, and shown semi-transparent for comparison. A water molecule that is accessible to bulk solvent and is proposed to be involved in the reaction mechanism is shown as a red sphere.

Figure 5

Relationship of halohydrin dehalogenases to the SDR family. (A) Superposition of 3α/20β-HSD (grey) with halohydrin dehalogenase HheC (green), showing a similar α/β fold architecture. (B) Close-up of the active sites of 3α/20β-HSD and HheC. Residues in the active site of 3α/20β-HSD and HheC are labeled in grey and green, respectively. The NAD molecule from 3α/20β-HSD is shown as well as the chloride ion bound to HheC.