Coenzyme binding in F420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family

F-420-dependent secondary alcohol dehydrogenase (Adf) from methanogenic archaea is a member of the growing bacterial luciferase family which are all TIM barrel enzymes, most of which with an unusual non-prolyl cis peptide bond. We report here on the crystal structure of Adf from Methanoculleus thermophilicus at 1.8 Angstrom resolution in complex with a F-420-acetone adduct. The knowledge of the F-420 binding mode in Adf provides the molecular basis for modeling F-420 and FMN into the other enzymes of the family. A non-prolyl cis peptide bond was identified as an essential part of a bulge that serves as backstop at the Re-face of F-420 to keep it in a bent conformation. The acetone moiety of the F-420-acetone adduct is positioned at the Si-face of F-420 deeply buried inside the protein. Isopropanol can be reliably modeled and a hydrogen transfer mechanism postulated. His39 and Glu108 can be identified as key players for binding of the acetone or isopropanol oxygens and for catalysis.