7TPJ

Single-Particle Cryo-EM Structure of the WaaL O-antigen ligase in its apo state

Summary for 7TPJ

• Entry DOI: 10.2210/pdb7tpj/pdb
• EMDB information: 26057
• Descriptor: Putative cell surface polysaccharide polymerase/ligase, Fab Heavy (H) Chain, Fab Light (L) Chain (3 entities in total)
• Functional Keywords: lipopolysaccharide, single-particle cryo-electron microscopy, molecular dynamics simulations, structural biology, undecaprenyl pyrophosphate, waal ligase, lipid a, o-antigen, membrane proteins, transglycosylation, glycosyltransferase, membrane protein
• Biological source: Cupriavidus metallidurans; More
• Total number of polymer chains: 3
• Total formula weight: 93010.82

Authors

Ashraf, K.U.,Nygaard, R.,Vickery, O.N.,Erramilli, S.K.,Herrera, C.M.,McConville, T.H.,Petrou, V.I.,Giacometti, S.I.,Dufrisne, M.B.,Nosol, K.,Zinkle, A.P.,Graham, C.L.B.,Loukeris, M.,Kloss, B.,Skorupinska-Tudek, K.,Swiezewska, E.,Roper, D.,Clarke, O.B.,Uhlemann, A.C.,Kossiakoff, A.A.,Trent, M.S.,Stansfeld, P.J.,Mancia, F. (deposition date: 2022-01-25, release date: 2022-04-06, Last modification date: 2024-10-23)

Primary citation

Ashraf, K.U.,Nygaard, R.,Vickery, O.N.,Erramilli, S.K.,Herrera, C.M.,McConville, T.H.,Petrou, V.I.,Giacometti, S.I.,Dufrisne, M.B.,Nosol, K.,Zinkle, A.P.,Graham, C.L.B.,Loukeris, M.,Kloss, B.,Skorupinska-Tudek, K.,Swiezewska, E.,Roper, D.I.,Clarke, O.B.,Uhlemann, A.C.,Kossiakoff, A.A.,Trent, M.S.,Stansfeld, P.J.,Mancia, F.
Structural basis of lipopolysaccharide maturation by the O-antigen ligase.
Nature, 604:371-376, 2022

PubMed Abstract: The outer membrane of Gram-negative bacteria has an external leaflet that is largely composed of lipopolysaccharide, which provides a selective permeation barrier, particularly against antimicrobials. The final and crucial step in the biosynthesis of lipopolysaccharide is the addition of a species-dependent O-antigen to the lipid A core oligosaccharide, which is catalysed by the O-antigen ligase WaaL. Here we present structures of WaaL from Cupriavidus metallidurans, both in the apo state and in complex with its lipid carrier undecaprenyl pyrophosphate, determined by single-particle cryo-electron microscopy. The structures reveal that WaaL comprises 12 transmembrane helices and a predominantly α-helical periplasmic region, which we show contains many of the conserved residues that are required for catalysis. We observe a conserved fold within the GT-C family of glycosyltransferases and hypothesize that they have a common mechanism for shuttling the undecaprenyl-based carrier to and from the active site. The structures, combined with genetic, biochemical, bioinformatics and molecular dynamics simulation experiments, offer molecular details on how the ligands come in apposition, and allows us to propose a mechanistic model for catalysis. Together, our work provides a structural basis for lipopolysaccharide maturation in a member of the GT-C superfamily of glycosyltransferases.

PubMed: 35388216
DOI: 10.1038/s41586-022-04555-x

Experimental method

ELECTRON MICROSCOPY (3.46 Å)