Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

Abstract

Serine hydroxymethyltransferase (SHMT) is a ubiquitous enzyme belonging to the fold type I or aspartate aminotransferase (AspAT) family of the pyridoxal 5′-phosphate (PLP)dependent enzymes. Like other PLP-dependent enzymes, SHMT also undergoes the so-called transimination reaction before exhibiting its enzymatic activity. The transimination process constitutes an important pre-step for all PLP-dependent enzymes, where an internal aldimine of the PLP−enzyme complex gets converted to an external aldimine of the substrate−PLP complex at the active site of the enzyme. In case of the transimination reaction involving SHMT, the PLP molecule bound to the active site lysine residue of SHMT (internal aldimine) gets detached from the enzyme by a serine substrate to produce an external aldimine complex, where the PLP is now bound to the serine substrate. In the current study, the free energy surfaces and reaction pathways of different steps of the transimination reaction at the active site of SHMT are investigated by employing hybrid quantum mechanical/molecular mechanical (QM/MM) simulations combined with metadynamics methods of rare event sampling. It is found that the process of transimination involving serine and PLP at the active site of the SHMT enzyme takes place through different elementary steps such as the formation of the first geminal diamine intermediate (GDI1), transfer of a proton from the substrate serine to the phenolic oxygen of PLP, followed by another proton transfer from PLP to the amine nitrogen of lysine with the formation of the second geminal diamine intermediate (GDI2), and finally, detachment of the active site lysine residue from PLP to produce the external aldimine.

Revealing protonation states and tracking substrate in serine hydroxymethyltransferase with room-temperature X-ray and neutron crystallography

“…Identical protonation states for PLP in the internal aldimine state have been observed in the joint XN structure of AAT 44 . In disagreement with our experimental results, however, several published theoretical calculations of the SHMT catalytic mechanism used protonated, positively charged, N SB in the internal aldimine state 60 , 83 , 84 . In order to proceed through the transaldimination reaction, the incoming amino acid substrate needs to be deprotonated.…”