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Biotechnology and Bioengineering, Vol.110, No.11, 2803-2814, 2013
Crystallographic Analysis and Structure-Guided Engineering of NADPH-Dependent Ralstonia sp Alcohol Dehydrogenase Toward NADH Cosubstrate Specificity
The NADP(+)-dependent alcohol dehydrogenase from Ralstonia sp. (RasADH) belongs to the protein superfamily of short-chain dehydrogenases/reductases (SDRs). As an enzyme that accepts different types of substratesincluding bulky-bulky as well as small-bulky secondary alcohols or ketoneswith high stereoselectivity, it offers potential as a biocatalyst for industrial biotechnology. To understand substrate and cosubstrate specificities of RasADH we determined the crystal structure of the apo-enzyme as well as its NADP(+)-bound state with resolutions down to 2.8 angstrom. RasADH displays a homotetrameric quaternary structure that can be described as a dimer of homodimers while in each subunit a seven-stranded parallel -sheet, flanked by three -helices on each side, forms a Rossmann fold-type dinucleotide binding domain. Docking of the well-known substrate (S)-1-phenylethanol clearly revealed the structural determinants of stereospecificity. To favor practical RasADH application in the context of established cofactor recycling systems, for example, those involving an NADH-dependent amino acid dehydrogenase, we attempted to rationally change its cosubstrate specificity from NADP(+) to NAD(+) utilizing the structural information that NADP(+) specificity is largely governed by the residues Asn15, Gly37, Arg38, and Arg39. Furthermore, an extensive sequence alignment with homologous dehydrogenases that have different cosubstrate specificities revealed a modified general SDR motif ASNG (instead of NNAG) at positions 86-89 of RasADH. Consequently, we constructed mutant enzymes with one (G37D), four (N15G/G37D/R38V/R39S), and six (N15G/G37D/R38V/R39S/A86N/S88A) amino acid exchanges. RasADH (N15G/G37D/R38V/R39S) was better able to accept NAD(+) while showing much reduced catalytic efficiency with NADP(+), leading to a change in NADH/NADPH specificity by a factor of approximate to 3.6 million. Biotechnol. Biotechnol. Bioeng. 2013;110: 2803-2814. (c) 2013 Wiley Periodicals, Inc.