NMR solution structure of the integral membrane enzyme DsbB: functional insights into DsbB-catalyzed disulfide bond formation

Abstract

We describe the NMR structure of DsbB, a polytopic helical membrane protein. DsbB, a bacterial cytoplasmic membrane protein, plays a key role in disulfide bond formation. It reoxidizes DsbA, the periplasmic protein disulfide oxidant, using the oxidizing power of membrane-embedded quinones. We determined the structure of an interloop disulfide bond form of DsbB, an intermediate in catalysis. Analysis of the structure and interactions with substrates DsbA and quinone reveals functionally relevant changes induced by these substrates. Analysis of the structure, dynamics measurements, and NMR chemical shifts around the interloop disulfide bond suggest how electron movement from DsbA to quinone through DsbB is regulated and facilitated. Our results demonstrate the extraordinary utility of NMR for functional characterization of polytopic integral membrane proteins and provide insights into the mechanism of DsbB catalysis.

Figure 1. Mechanism of DsbB catalyzed DsbA oxidation

(A) Schematic representation of steps in DsbB catalyzed DsbA oxidation. (B) TROSY-based ¹⁵N-¹H HSQC spectrum (500 MHz) of protonated wildtype DsbB and (C) DsbB[CSSC] in DPC micelles.

Figure 2. Structure of DsbB[CSSC]

(A) Ribbon representation of the structure of DsbB[CSSC] viewed from the periplasmic end. The inter-loop disulfide bond (Cys41-Cys130) is in yellow. (B) Ribbon representation of the structure of DsbB viewed from the membrane plane. (C) Overlay of 20 conformers of DsbB[CSSC] viewed from the periplasmic end, with α-helices in blue, β-strands in red, disulfide bond in yellow. (D) Overlay of 20 conformers of DsbB[CSSC] viewed from the membrane plane. (E) Overlay of DsbB NMR structure (blue) and crystal structure (red) viewed from the periplasmic end. (F) Overlay of DsbB NMR and crystal structure viewed from the membrane plane.

Figure 3. Docking of DsbB[CSSC] into a POPC lipid bilayer and periplasmic loop dynamics

(A) Structure of DsbB[CSSC] docked into a POPC bilayer using EPR measurements. Black planes represent the level of the phosphate head group and green are individual phosholipid molecules from a molecular dynamics simulation. (B) Close-up view of DsbB[CSSC] docked into a POPC bilayer. (C) Plot of ¹⁵N-{¹H} heteronuclear NOEs versus the primary sequence. PL2 (aa 97–115) and PL2’ (aa 120–135) are indicated with gray shadow. Depressed values in the N-terminus of PL2 (aa 99–105) indicate increased mobility in this region.

Fig. 4. DsbA binding and model of DsbB-DsbA complex

(A) TROSY-HSQC spectra of DsbB[CSSC] in the presence (red) and in the absence (blue) of DsbA[SS]. (B) Mapping of NH chemical shift changes upon DsbA titration. Strong (>20 Hz), medium (8–20 Hz), and weak (<8 Hz) changes are colored red, orange, and blue, respectively. Residues with no information are colored gray. (C) Selected region of the saturation transfer TROSY-HSQC for saturation transfer from DPC to DsbB[CSSC]. (D) Selected region of the saturation transfer TROSY-HSQC for saturation transfer from DsbA[SS] and DPC to DsbB[CSSC] (see also Figure S9). (E) Model of DsbB-DsbA complex with rearranged intermolecular and inter-loop disulfide bonds. DsbA, the hinge loop between the thioredoxin and α-helical domains in DsbA, and PL2 of DsbB from the crystal structure are shown as green, pink, and cyan respectively. DsbB from the solution structure, with the exception of PL2, is shown as a blue ribbon. The six essential Cys residues are colored yellow. UQ2 is shown in a ball-and-stick representation. Gly128 and Glu129 (red space filling repesentation) of DsbB, which show significant chemical shift perturbations in DsbA titration experiment, are in close proximity to Met64 and Gly65 (pink space filling representation) in the hinge loop in DsbA. (F) Close-up view of the model of DsbB-DsbA complex. The six essential Cys residues are numbered.

Fig. 5. The Cys41-Cys130 inter-loop disulfide bond

(A) Closeup view of the Cys41-Cys130 disulfide bond. (B) Scheme of interactions around the inter-loop disulfide bond. The + and − signs refer to the TM2 helix dipole. The δ+ indicates the partial positive charge at the Cys41 sulfur. The oval is a schematic representation of the electron density around the disulfide bond.

Fig. 6. Characterization of the UQ binding site

(A) TROSY-based ¹⁵N-¹H HSQC spectrum of UQ-free DsbB[CSSC]. (B) TROSY-based ¹⁵N-¹H HSQC spectrum of DsbB[CSSC]-UQ2. (C, D) Overlay of 20 conformers of the solution structure of the DsbB[CSSC] – UQ2 complex (DsbB in blue, carbon and oxygen atoms of UQ2 in black and red). The DsbB crystal structure and proposed quinone orientation is also shown (DsbB in green, carbon and oxygen atoms of UQ in ivory and red). For clarity, both are shown from two different angles. (E) Ribbon representation of the DsbB[CSSC] – UQ2 complex. UQ2 is shown in a ball-and-stick representation. Carbon and oxygen atoms of UQ2 are colored black and red, respectively. (F) Close-up view of the UQ binding site on DsbB. Sidechains of quinone interacting residues are shown and labeled (Gln33, Cys44, Arg48, Met142).