Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase

YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The ensemble of NADPH-bound monomers has a narrower average interdomain space resulting in more hydrogen bonds and rigid cofactor binding. NADP-bound YqhD fluctuates between open and closed conformations, while it was observed that NADPH-bound YqhD had slower opening/closing dynamics of the cofactor-binding cleft. In the light of enzyme kinetics and structural data, simulation findings have led us to postulate that the frequently sampled open conformation of the cofactor binding cleft with NADP leads to the more facile release of NADP while increased closed conformation sampling during NADPH binding enhances cofactor binding affinity and the aldehyde reductase activity of the enzyme.

Automated summary

YqhD, an enzyme from E. coli, produces valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. The oxidized and reduced states of the NADP/H cofactor binding influence the conformational dynamics of the enzyme, with NADPH-bound monomers having a tighter interdomain space and more rigid cofactor binding compared to NADP-bound monomers. The enzyme's aldehyde reductase activity is enhanced by increased closed conformation sampling during NADPH binding.