Understanding oligomerization in 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni: an in silico approach and evidence for an active protein.

3alpha-Hydroxysteroid dehydrogenase/carbonyl reductase (3alpha-HSD/CR) from Comamonas testosteroni belongs to the short chain dehydrogenase/reductase (SDR) protein superfamily and catalyzes the oxidoreduction of a variety of steroid substrates, including the steroid antibiotic fusidic acid. The enzyme also mediates the carbonyl reduction of non-steroidal aldehydes and ketones such as a novel insecticide. It is suggested that 3alpha-HSD/CR contributes to the bioremediation of natural and synthetic toxicants by C. testosteroni. Crystallization and structure analysis showed that 3alpha-HSD/CR is active as a dimer. Dimerization takes place via an interface axis which has exclusively been observed in homotetrameric SDRs but never in the structure of a homodimeric SDR. The formation of a tetramer is blocked in 3alpha-HSD/CR by the presence of a predominantly alpha-helical subdomain which is missing in all other SDRs of known structure. For example, 3alpha/20beta-HSD from Streptomyces hydrogenans exhibits two main subunit interfaces arranged about two non-crystallographic two-fold axes which are perpendicular to each other and referred to as P and Q. This mode of dimerization is, however, sterically impossible in 3alpha-HSD/CR because of a 28 amino acids insertion into the classical Rossmann-fold motif between strand betaE and helix alphaF. This insertion is masking helices alphaE and alphaF, thus preventing the formation of a four helix bundle and enables the dimerization via a P-axis interface. This type of dimerization in SDRs has never been observed in a crystal structure so far. The aim of this study was to investigate whether the lack of this predominantly alpha-helical subdomain keeps 3alpha-HSD/CR to be an active enzyme and whether, by an in silico approach, the formation of a homotetramer or even a novel oligomerization mode can be expected. Redesign of this interface was performed on the basis of site directed mutagenesis and according to other SDR structures by an approach combining "in silico" and "wet chemistry". Simulations of sterical and structural effects after different mutations, by applying a combination of homology modelling and molecular dynamic simulations, provided an effective tool for extensive mutagenesis studies and indicated the possibility of tetramer formation of truncated 3alpha-HSD/CR. In addition, despite lacking the extra loop domain, mutant 3alpha-HSD/CR was shown to be active towards a variety of standard substrates.