Monotopic Membrane Proteins Join the Fold

Abstract

Monotopic membrane proteins, classified by topology, are proteins that embed into a single face of the membrane. These proteins are generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has revealed new examples that allow the description of generalizable features. This Opinion article summarizes shared characteristics including oligomerization states, modes of membrane association, mechanisms of interaction with hydrophobic or amphiphilic substrates, and homology to soluble folds. We also discuss how associations of monotopic enzymes in pathways can be used to promote substrate specificity and product composition. These examples highlight the challenges in structure determination specific to this class of proteins, but also the promise of new understanding from future study of these proteins that reside at the interface.

Keywords: membrane interface; membrane–protein interaction; membranome; monotopic enzymes.

Figure 1

Structures of representative monotopic membrane enzymes. Protein surface colored by normalized consensus hydrophobicity from hydrophobic (red) to hydrophilic (white). Membrane represented by gray box. Location of membrane plane calculated with PPM server (http://opm.phar.umich.edu/server.php) for 1CQE (COX-2), 2SQC (SHC), 2QCU (GlpD), 2H4T (CPT-II), 5KYM (PlsC), 2XC1 (WaaA), 5W7L (PglC), and 3EQM (CYP19A1).

Figure 2

Comparison of membrane proteins and their soluble homologues. Ribbon diagram of membrane proteins (purple) superimposed with the fold core of a prototypical soluble homologue (gray). Red dashed line indicates approximate membrane location calculated using the PPM server [49]. (A) lysophosphatidic acid acyltransferase, PlsC (purple, 5KYM) and glycerol-3-phosphate (1)-acyltransferase (gray, 1K30); (B) tetraacyldisaccharide-1-phosphate 4’-kinase, LpxK (purple, 4EHW) and GTP-binding protein HypB (gray, 2HF9); (C) fatty acid alpha-deoxygenase, α-DOX (purple, 4HHS) and myeloperoxidase (gray, 1CXP) with heme group in pink space-filling.

Figure 3

Reactions of structurally-characterized monotopic membrane enzymes. (A) Hydrolysis and alkene isomerization by RPE65; (B) COX-2 – prostaglandin endoperoxide synthase; (C) α–DOX, linoleic acid α-hydroperoxidase; (D) SHC Squalene-hopene cyclase; (E) GlpD – FAD-dependent oxidation of glycerol-3-phosphate; (F) PlsC lysophosphatidic acid acyltransferase; (G) Steps in the Campylobacter jejuni protein glycosylation pathway – phosphoglycosyl transferase PglC and glycosyl transferases PglA, PglJ and PglH; (H) Steps in the E. coli pathway for Lipid A biosynthesis, focusing on kinase LpxK and glycosyl transferase WaaA. Yellow highlighting in (G) and (H) emphasizes moieties with significant hydrophobic character.

Figure 4

Insight into GTase and kinase interactions with membrane calculated using the PPM server. (A) GTase interaction with the membrane changes based on glycosyl acceptor substrate: (Left) WbnH (4XYW) transfers GalNAc to membrane-resident Pren-PP-GalNAc, (right) PglH (6EJK) shown bound to non-hydrolyzable UDP-CH₂-GalNAc (spheres) sequentially transfers three GalNAcs to membrane-resident Pren-PP-trisaccharide. C-terminal GT-B domain (pink), N-terminal GT-B domain (pale blue), bracing helix (pale green), membrane-interacting residues (slate blue), membrane surface (red), active-site cleft red asterix; (B) LpxK kinase changes conformation on binding to ADP-Mg²⁺ Protein colored N- to C-terminus (rainbow), membrane-associated residues (slate blue). (Left) Open form of LpxK. (Right) Closed form bound to ADP-Mg²⁺. ADP (space filling colored by atom), Mg²⁺ gray sphere. Red arrow shows movement of the C-terminal domain.