Catalytically requisite conformational dynamics in the mRNA-capping enzyme probed by targeted molecular dynamics

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• mRNA capping is crucial for eukaryotic gene expression, involving the N7-methyl guanosine cap addition by a specific enzyme.
• The mRNA-capping enzyme possesses two domains: a catalytic nucleotidyltransferase domain and a noncatalytic oligonucleotide/oligosaccharide binding (OB) domain.
• Substrate binding induces large-scale domain motion, rearranging the GTP substrate for catalysis.

Purpose of the Study:

• To investigate the global and internal dynamics of the PBCV-1 mRNA-capping enzyme during its conformational transition from open to closed states.
• To elucidate the conserved mechanism of conformational rearrangement in mRNA-capping enzymes and ATP-dependent DNA ligases.

Main Methods:

• Targeted molecular dynamics (TMD) simulations were used to analyze domain motion and internal residue dynamics.
• Structural and sequence homology analysis was performed across related enzymes.

Main Results:

• The OB domain moves quasi-statically towards the nucleotidyltransferase domain, pivoting on a linker region.
• This movement brings a conserved RxDK sequence (motif VI) near the GTP triphosphate.
• This proximity destabilizes the unreactive GTP conformation, facilitating thermal fluctuations towards a catalytically competent state.

Conclusions:

• A conserved mechanism for conformational rearrangement exists in mRNA-capping enzymes and ATP-dependent DNA ligases.
• The OB domain's movement is key to GTP substrate activation prior to the chemical step.
• Understanding these dynamics provides insights into enzyme catalysis and potential drug targets.