Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420:: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family

Methylenetetratetrahydromethanopterin reductase (Mer) is involved in CO2 reduction to methane in methanogenic archaea and catalyses the reversible reduction of methylenetetrahydromethanopterin (methylene-H4MPT) to methyl-H4MPT with coenzyme F420H2, which is a reduced 5'-deazaflavin. Mer was recently established as a TIM barrel structure containing a nonprolyl cis-peptide bond but the binding site of the substrates remained elusive. We report here on the crystal structure of Met in complex with F-420 at 2.6 angstrom resolution. The isoalloxazine ring is present in a pronounced butterfly conformation, being induced from the Re-face of F-420 by a bulge that contains the non-prolyl cis-peptide bond. The binding mode of F-420 is very similar to that in F-420-dependent alcohol dehydrogenase Adf despite the low sequence identity of 21%. Moreover, binding of F-420 to the apoenzyme was only associated with minor conformational changes of the polypeptide chain. These findings allowed us to build an improved model of FMN into its binding site in bacterial luciferase, which belongs to the same structural family as Mer and Adf and also contains a nonprolyl cis-peptide bond in an equivalent position.