Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step

Abstract

Molecular shuttles play decisive roles in many multi-enzyme systems such as the glycine cleavage system (GCS) for one-carbon (C1) metabolism. In GCS, a lipoate swinging arm containing an aminomethyl moiety is attached to protein H and serves as a molecular shuttle among different proteins. Protection of the aminomethyl moiety in a cavity of protein H and its release induced by protein T are key processes but barely understood. Here, we present a detailed structure-based dynamic analysis of the induced release of the lipoate arm of protein H. Based on molecular dynamics simulations of interactions between proteins H and T, four major steps of the release process showing significantly different energy barriers and time scales can be distinguished. Mutations of a key residue, Ser-67 in protein H, led to a bidirectional tuning of the release process. This work opens ways to target C1 metabolism in biomedicine and the utilization of formate and CO2 for biosynthesis.

Improvement of glycine biosynthesis from one‐carbon compounds and ammonia catalyzed by the glycine cleavage system in vitro

“…Recently, our group has studied the catalytic mechanism related to interactions between H protein and other GCS proteins. Zhang et al [33] presented a detailed molecular dynamics (MD) analysis of the interactions within the E. coli H-T protein complex that governs the induced release of the aminomethyl lipoate arm from a protected state in the cavity of H protein.…”

“…Zhang et al. [ 33 ] presented a detailed molecular dynamics (MD) analysis of the interactions within the E. coli H‐T protein complex that governs the induced release of the aminomethyl lipoate arm from a protected state in the cavity of H protein.…”

Pathogenic variants inGCSHencoding the moonlighting H-protein cause combined nonketotic hyperglycinemia and lipoate deficiency

“…Our study only examined the interaction with the P-protein through the glycine exchange reaction, and not the interaction with T-protein, or a direct study of its interaction with the lipoyltransferase LIPT2. Variants could also affect the reaction of the swinging lipoyl-arm to protect the amino-methyl group, for which Ser67 is important ( 32 ).…”

Enzymatic Conversion of CO2: From Natural to Artificial Utilization

“…Finally, the pyridoxal-5′-phosphate (PLP)-dependent P-protein catalyzes the reductive carboxylation step in which CO 2 is reduced, while the lipoic acid in the H-protein is reoxidized to form a disulfide. Recently, a detailed molecular dynamics-based study investigated the protection and T-protein-mediated release of the aminomethylation on the lipoate arm . This provided crucial insights into the mechanisms responsible for guiding the reaction along the desired reaction trajectory and showed that aminomethylation release from the lipoate arm is the rate-limiting step of the GCS reaction .…”