Structural basis for catalysis at the membrane-water interface

Abstract

The membrane-water interface forms a uniquely heterogeneous and geometrically constrained environment for enzymatic catalysis. Integral membrane enzymes sample three environments - the uniformly hydrophobic interior of the membrane, the aqueous extramembrane region, and the fuzzy, amphipathic interfacial region formed by the tightly packed headgroups of the components of the lipid bilayer. Depending on the nature of the substrates and the location of the site of chemical modification, catalysis may occur in each of these environments. The availability of structural information for alpha-helical enzyme families from each of these classes, as well as several beta-barrel enzymes from the bacterial outer membrane, has allowed us to review here the different ways in which each enzyme fold has adapted to the nature of the substrates, products, and the unique environment of the membrane. Our focus here is on enzymes that process lipidic substrates. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.

Figure 1. Schematic representation of the different catalytic modes at the membrane-water interface

The grey region represents the membrane. The green rectangle represents the transmembrane domain of an enzyme (TMD), the orange teardrop represents a soluble domain (SD), and the yellow circle represents the location of the active site (AS).

Figure 2. Representative structures showing Interfacial catalysis (I)

All structures are shown in ribbon representation with bound ligands shown in CPK representation. Transmembrane domains are shown in gradient coloring from the N-terminus to the C-terminus (blue to cyan to green) while extramembrane soluble domains are shown in orange. Grey square shows approximate location of the membrane border. Pale yellow circle indicates location of the putative active site. All structures are oriented with the cytosolic face of the membrane on the bottom. A schematic of the reaction catalyzed is shown above each structure. A. Phosphatidylinositol-phosphate synthase (PIP-synthase; PDB 5D92) with four aspartate residues from the CDP-AP signature sequence in red responsible for metal coordination and catalysis. Magnesium ion in light green and lipid CDP-diacylglycerol (CDP-DAG) in magenta. CDP-DAG, cytidine diphosphate diacylglycerol; IP, inositol-phosophate; PIP, phosphatidylinositol-phosphate; CMP, cytidine monophosphate. B. Isoprenylcysteine carboxyl methyltransferase (ICMT; PDB 4A2N) with putative catalytic residue in red. Methyl donor product S-Adenosyl-homocysteine (SAH) in magenta. SAM, S-Adenosyl methionine C. CDP-DAG synthetase (CdsA; PDB 4Q2E) with putative metal binding and catalytic residues in red. Magnesium ion in light green. Potassium ion in purple. PA, phosphatidic acid; CTP, cytidine triphosphate. D. Diacylglycerol kinase (DgkA; PDB 4UXX) with putative catalytic residue in red. Monoacylglycerol (MAG) in magenta, adenylmethylenediphosphonate (ACP) in purple, two zinc ion in yellow (partially obscured by ACP). E. Vitamin K epoxide reductase (VKOR; PDB 3KP9) cysteines proposed in electron transfer in red. Ubiquinone (UQ) in magenta. VK, vitamin K. F. Phosphatidylglycerolphosphate phosphatase B (PgpB; PDB 4PX7) with putative catalytic residues in red.

Figure 3. Representative structures showing Interfacial catalysis (II)

All structures are shown in ribbon representation with bound ligands shown in CPK representation. Transmembrane domains are shown in gradient coloring from the N-terminus to the C-terminus (blue to cyan to green), while extramembrane soluble domains are shown in orange. The grey square shows the approximate location of the membrane border. The pale yellow circle indicates the location of the putative active site. All structures oriented with the cytosolic face of the membrane on the bottom. A. Phospho-MurNAc-pentapeptide translocase (MraY; PDB 4J72) with putative catalytic residues in red. Nickel ion in pink, magnesium ion in light green. UDP, uridine diphosphate; UMP uridine monophosphate; UndP, undecaprenyl phosphate. B. A4-amino-4-deoxy-L-arabinose transferase (ArnT; PDB 5F15) with putative catalytic residues in red. UndP in magenta. C. Lipoprotein diacylglycerol transferase (Lgt; PDB 5A2C) with putative catalytic residues in red. Phosphatidylglycerol (PG) in magneta. D. Prenyltransferase UbiA (PDB 4OD5) with putative catalytic residues in red. Geranyl thiolopyrophosphate (GSPP) in magenta, p-hydroxybenzoate (PHB) in purple, magnesium ions in yellow. A1 and A2, arm 1 and arm 2; IPP, isoprenylpyrophosphate; UQ, ubiquinone. E. Leukotriene C₄ Synthase (LTC4S; PDB 4J7T) with putative catalytic residue in red. Leukotriene (LT) analog in magenta. LTA4, (5S)-trans-5,6-oxido-7,9-trans-11,14-cis-eicosatetraenoic acid; LTC4, (6R)-S-glutathionyl-7,9-trans-11,14-cis-eicosatetraenoic acid ; GSH, glutathione.

Figure 4. Representative structures showing extramembrane catalysis

All structures are shown in ribbon representation with bound ligands shown in CPK representation. Transmembrane domains are shown in gradient coloring from the N-terminus to the C-terminus (blue to cyan to green), while extramembrane soluble domains are shown in orange. The grey square shows the approximate location of the membrane border. The pale yellow circle indicates the location of the putative active site. All structures oriented with the cytosolic face of the membrane on the bottom. A. Polyisoprenyl glycosyltransferase GtrB (PDB 5EKP) with putative metal biding and catalytic residues in red. Magnesium ion in light green. UndP, undecaprenyl phosphate; UDP, uridine diphosphate. B. Steroid sulfatase (STS; PDB 1P49) with formylglycine-sulfate (FGly; modified cysteine residue) in red. Calcium ion in light green. C. Transglycosylase (TG; PDB 3VMT) with putative catalytic and metal binding residues in red. Lipid II analog in magenta and magnesium ions in light green. UndPP, undecaprenyl pyrophosphate. D. Stearoyl-CoA desaturase (SCD1; PDB 4YMK) with zinc ions (indicating the di-iron center) in green. Stearoyl-CoA in magenta. E. Oligosaccharyltransferase PglB (PDB 3RCE) putative metal binding and catalytic residues in red. Oligosaccharide acceptor peptide in purple, magnesium ions in yellow. EL, external loop.

Figure 5. Representative structure showing intramembrane catalysis

Sterol reductase (SR1; PDB 4QUV) with putative catalytic residues in red. Cofactor NADPH in purple in CPK representation. Structure is shown in ribbon representation colored in a gradient from the N-terminus to the C-terminus (blue to cyan to green). The grey square shows the approximate location of the membrane border. The pale yellow circle indicates the location of the putative active site. The protein is oriented with the cytoplasmic face of the membrane on the bottom.

Figure 6. Representative structures of integral membrane beta-barrel enzymes

All structures are shown in ribbon representation with bound ligands in CPK representation. The proteins are colored with a gradient from the N-terminus to the C-terminus (blue to cyan to green). The grey square shows the approximate location of the membrane border. The pale yellow circle indicates the location of the putative active site. All structures oriented with the periplamic face of the membrane on the bottom. A. Outer membrane phospholipase (OMPLA; PDB 1QD6). The inhibitor hexadecanesulphonyl fluoride (HDS) is covalently bound to the nucleophilic serine residue (S144; shown in red). The catalytic calcium ion is shown in yellow. PE, phosphatidylethanolamine. B. Plasminogen activator protease (Pla; PDB 2X55). Observed bound acyl chains represented as C₈E₄ detergent chains potentially correspond to bound Lipid A with partial occupancy (shown in magenta). Putative catalytic and LPS-binding residues shown in red. C. Palmitoyltransferase (PagP; PDB 1THQ) with bound LDAO detergent molecule in the hydrocarbon ruler pocket. LDAO shown in magenta. PC, phosphatidylcholine; Lipid B, hepta-acylated Lipid A. D. Deacylase PagL (PDB 2ERV). Putative catalytic residues are shown in red. E. Deacylase LpxR (PDB 3FID). Putative catalytic and Kdo sugar binding residues are shown in red. Zinc ion observed in the structure is shown in yellow.