A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

Abstract

Acylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance to viruses and antimicrobials, and biosynthesis of antibiotics, yet their structure and mechanism are largely unknown. In this study, evolutionary co-variance analysis was used to build a computational model of the structure of a bacterial O-antigen modifying acetyltransferase, OafB. The resulting structure exhibited a novel fold for the AT3 domain, which molecular dynamics simulations demonstrated is stable in the membrane. The AT3 domain contains 10 transmembrane helices arranged to form a large cytoplasmic cavity lined by residues known to be essential for function. Further molecular dynamics simulations support a model where the acyl-coA donor spans the membrane through accessing a pore created by movement of an important loop capping the inner cavity, enabling OafB to present the acetyl group close to the likely catalytic resides on the extracytoplasmic surface. Limited but important interactions with the fused SGNH domain in OafB are identified, and modelling suggests this domain is mobile and can both accept acyl-groups from the AT3 and then reach beyond the membrane to reach acceptor substrates. Together this new general model of AT3 function provides a framework for the development of inhibitors that could abrogate critical functions of bacterial pathogens.

Structure of the human heparan-α-glucosaminideN-acetyltransferase (HGSNAT)

“…However, based on AlphaFold prediction, this extra-membranous domain seems to be a α-β-α sandwich with a single 5-stranded β-sheet sandwiched between two helical domains. Incidentally, a bent helix near the predicted acetyl-CoA binding site is also observed in the ATAT family, suggesting that this could be a conserved feature amongst the members of TmAT superfamily (Newman et al , 2023). We used ConSurf to estimate sequence conservation in HGSNAT based on an automatic sequence alignment algorithm (Ashkenazy et al , 2016).…”

“…We see unexplained density in these regions that could be best explained as ordered lipids or digitonin (Fig S7). A recent report of a computational modeling and molecular dynamics simulation study conducted on a model of OafB, a bacterial O-antigen modifying transmembrane acetyltransferase of the ATAT family within the TmAT superfamily, showed that the periplasmic SGNH domain undergoes large conformational changes and aid in O-antigen acetylation (Newman et al, 2023). OafB has two domains – the transmembrane acetyltransferase-3 domain (AT-3) and periplasmic SGNH domain.…”

Bioinformatics Analysis Identifies Potential Hub Genes, Therapeutic Agents, and Crucial Pathways in the Pathogenesis of Refsum's Disease

“…Phytanoyl-CoA hydroxylase is part of a process that breaks down phytanic acid in peroxisomes. Hence, enzyme is perilous for the normal function of cell structures called peroxisomes (Newman et al, 2023). Another hub gene from module 1, that is, carnitine acyltransferases, effectuates the swapping of acyl groups among carnitine and CoA.…”