Structure of an EIIC sugar transporter trapped in an inward-facing conformation

Zhenning Ren; Jumin Lee; Mahdi Muhammad Moosa; Yin Nian; Liya Hu; Zhichun Xu; Jason G. McCoy; Allan Chris M. Ferreon; Wonpil Im; Ming Zhou

doi:10.1073/pnas.1800647115

New Research In

Edited by Ernest M. Wright, David Geffen School of Medicine at UCLA, Los Angeles, CA, and approved April 30, 2018 (received for review January 12, 2018)

Significance

The phosphoenolpyruvate-dependent phosphotransferase system (PTS) is a multiprotein system unique to bacteria. The PTS transports sugars into bacteria and then phosphorylates the sugars. Phosphorylation prevents sugars from escaping the cell and primes them for metabolic consumption. As a major component of the PTS, Enzyme IIC (EIIC) transports sugar across the membrane and assists the phosphorylation process, but the molecular mechanism of EIIC-mediated sugar transport is unclear. Results from this study allow visualization of conformational changes during sugar transport and establish the mechanism of transport at the atomic level. The knowledge will facilitate development of inhibitors against EIIC and provide a foundation for understanding the phosphorylation process.

Abstract

The phosphoenolpyruvate-dependent phosphotransferase system (PTS) transports sugar into bacteria and phosphorylates the sugar for metabolic consumption. The PTS is important for the survival of bacteria and thus a potential target for antibiotics, but its mechanism of sugar uptake and phosphorylation remains unclear. The PTS is composed of multiple proteins, and the membrane-embedded Enzyme IIC (EIIC) component transports sugars across the membrane. Crystal structures of two members of the glucose superfamily of EIICs, bcChbC and bcMalT, were solved in the inward-facing and outward-facing conformations, and the structures suggest that sugar translocation could be achieved by movement of a structured domain that contains the sugar-binding site. However, different conformations have not been captured on the same transporter to allow precise description of the conformational changes. Here we present a crystal structure of bcMalT trapped in an inward-facing conformation by a mercury ion that bridges two strategically placed cysteine residues. The structure allows direct comparison of the outward- and inward-facing conformations and reveals a large rigid-body motion of the sugar-binding domain and other conformational changes that accompany the rigid-body motion. All-atom molecular dynamics simulations show that the inward-facing structure is stable with or without the cross-linking. The conformational changes were further validated by single-molecule Föster resonance energy transfer (smFRET). Combined, these results establish the elevator-type mechanism of transport in the glucose superfamily of EIIC transporters.

The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) is ubiquitous in bacteria. The membrane-embedded component EIIC transports a sugar from the periplasmic side to the cytoplasmic side where the sugar is phosphorylated by the EIIB protein and then released into the cytoplasm. Phosphorylation occurs while the sugar is still bound to EIIC, and the phosphorylation facilitates the release of the sugar (1). The phosphate group originates from phosphoenolpyruvate and is transferred sequentially through four soluble phosphocarrier proteins, enzyme I (EI), the histidine phosphocarrier protein (HPr), enzyme IIA (EIIA), and enzyme IIB (EIIB) and eventually reaches the incoming sugar while it is still bound on EIIC (SI Appendix, Fig. S1). Phosphorylation of the incoming sugar helps maintain its concentration gradient to sustain the uptake, and the energy stored in the phosphate bond is recovered when the sugar is metabolized (2 ⇓⇓–5). Thus, EII systems are more efficient than other membrane-embedded transporters that either hydrolyze ATP or dissipate an ion gradient. EII systems have been categorized into four superfamilies, of which the largest is the glucose superfamily (6) and the focus of this research. Each EII has its own preference for a group of sugar molecules and is composed of three proteins, EIIA, B, and C. In some of the EIIs, EIIB and C, or EIIA, B, and C form a single polypeptide. Crystal structures of two EIICs from the glucose superfamily (7, 8) and one from the ascorbate and galactitol superfamily (9) have been reported. Several electron microscopy projection maps of two EIICs from the glucose superfamily have also been reported (10 ⇓–12). While members of the same superfamily share the same structural fold, those from different superfamilies do not.

Structures of an N,N′-diacetylchitobiose EIIC transporter bcChbC (7) and a maltose EIIC transporter bcMalT (8), both from Bacillus cereus, have been reported. bcChbC and bcMalT share 19% sequence identity and 50% similarity, and yet both have the same structural fold with almost all of the secondary structural elements conserved (SI Appendix, Fig. S2 A–E). Both proteins are homodimers, and each protomer has 10 transmembrane (TM1-10) helices, two reentrant loops (HP1-2), and two amphipathic helices (AH1-2). These structural elements fold into two distinctive structural domains. The dimerization domain (also referred to as the interface domain), which consists of TM1-5 and AH1, forms an expansive dimer interface. The substrate-binding domain (also referred to as the transport domain), which is composed of TM6-10 and two reentrant loops (HP1-2), contains the sugar-binding site. In both structures, the sugar substrate is coordinated by residues from TM6, TM7, HP1, and HP2 (SI Appendix, Fig. S2B). The two domains are bridged by an amphipathic helix (AH2) (SI Appendix, Fig. S2 C and D).

The bcChbC and bcMalT structures represent different conformations required to complete a transport cycle (13). Based on the location of the substrate-binding site, bcChbC is in an inward-facing conformation, while bcMalT is in an outward-facing conformation (SI Appendix, Fig. S2A). When the two structures are aligned by their dimerization domains, it seems that the substrate-binding domain could carry the substrate across the membrane by a rigid-body motion. A similar elevator-type transport mechanism has also been reported in a number of secondary solute transporters including amino acid transporters (EAAT1 and Glt_Ph) (14 ⇓–16), bile acid transporters (ASBT) (17), proton sodium exchangers (NhaA) (18, 19), concentrative nucleotide transporters (CNT_NW) (20), and citrate transporters (vcINDY and SeCitS) (21, 22). These transporters have different structural folds, and yet they all transport substrates from one side of the cell membrane to the other by rigid-body motions of a substrate-binding domain.

Although by comparing the inward-facing bcChbC structure and the outward-facing bcMalT structure we can postulate that the glucose superfamily of EIICs have an elevator-type mechanism of transport, we need to visualize both conformations on the same transporter to reveal details of the conformational changes. To achieve this, we first generated a structural model of bcMalT in an inward-facing conformation by collective variable-based steered molecular dynamics (CVSMD) simulation (SI Appendix, Fig. S2F) using the bcChbC structure as a guide (23). During the simulation, the interface domain was kept static, and the substrate-binding domain was steered toward the inward-facing conformation. Since the substrate-binding domain moves relative to the interface domain, we expect distance changes between the two domains. Indeed, the CVSMD model shows that residues that are far away from each other in the outward-facing structure become closer, for example, residues T280 and D55 and residues N284 and E54 (SI Appendix, Fig. S2G). We then showed that the pairs of residues predicted to become closer to each other can be cross-linked by a mercury ion when mutated to cysteine residues and thus provide an experimental validation to the CVSMD model and the elevator-type mechanism of transport (23).

In this study, we solved the crystal structure of bcMalT cross-linked in an inward-facing conformation. The structure provides direct experimental evidence that the substrate-binding domain can undergo a rigid-body rotation toward the intracellular side. The structure also shows conformational changes in other regions of the transporter that accommodate the rigid-body movement of the substrate-binding domain. Since cross-linking of a pair of residues could potentially trap the structure into a conformation that may not be native, we did two experiments to examine whether the structure is distorted. First, we applied all-atom molecular dynamics simulations to the structure and found that the inward-facing conformation is stable even when the cross-linking constraint is released. Second, we estimated the distance between a pair of symmetry-related residues on the substrate-binding domain by single-molecule Föster resonance energy transfer (smFRET) and found that the distances between the two residues are consistent with those measured from the inward- and outward-facing structures.

Results

Trapping bcMalT in an Inward-Facing Conformation.

CVSMD was used to show that residues T280 on the substrate binding domain and D55 on the dimerization domain can move to within 12.4 Å of each other as opposed to 23.7 Å in the outward facing crystal structure (SI Appendix, Fig. S2G). Similarly, N284 on the substrate-binding domain and E54 on the dimerization domain are 26.7 Å away in the crystal structure and 13.1 Å in the CVSMD model. Both pairs can be cross-linked by a mercury ion when mutated to cysteines, thus confirming their proximity (23). Although we were not able to crystallize the cross-linked proteins, we were encouraged by the predictive power of the inward-facing model and tested additional pairs in the vicinity of the previous successful ones. The Cα atoms of the T280-E54 pair are 19.3 Å apart in outward-facing bcMalT and 9.6 Å apart in the inward-facing model. When both residues were mutated to cysteines (T280C-E54C) they can be cross-linked at low (micromolar) concentrations of Hg²⁺ and at a protein-to-mercury molar ratio of ∼1:1. The cross-linked protein migrates faster on SDS/PAGE (Fig. 1A, lanes 2 and 3). The cross-linking is complete within seconds (Fig. 1B). These results suggest that the two residues have a high probability of reaching proximity. We then showed that the cross-linking is specific to the two cysteine mutations because the reaction can be reversed by addition of reducing reagent β-mercaptoethanol (Fig. 1A, lane 6), prevented by pretreatment with N-ethyl maleimide that alkylates free cysteines (Fig. 1A, lane 4), and did not happen on single-cysteine mutations (SI Appendix, Fig. S3A).

Fig. 1.

Cross-linking of bcMalT(T280C-E54C). (A) SDS/PAGE analysis of bcMalT(T280C-E54C) under various conditions. Lanes: 1, molecular weight standard; 2, bcMalT(T280C-E54C) without any treatment; 3, bcMalT(T280C-E54C) treated with Hg²⁺. Cross-linked bcMalT migrates faster, and the band is marked as X-linked; 4, bcMalT(T280C-E54C), first treated with 2 mM N-ethyl maleimide (NEM) and then incubated with 1:1 molar ratio of Hg²⁺; 5, bcMalT(T280C-E54C) in the presence of 2 mM β-mercaptoethanol (β-ME); 6, bcMalT(T280C-E54C) treated with Hg²⁺ and then incubated with 2 mM β-ME. (B) Time course of Hg²⁺-induced cross-linking of bcMalT(T280C-E54C).

We then assessed the functions of the T280C-E54C double-cysteine mutation in bcMalT. The double mutant transports maltose through facilitated diffusion when reconstituted into liposomes, suggesting that the cysteine mutations do not affect the function of the protein significantly (SI Appendix, Fig. S3B). We also found that the double-cysteine mutant binds to maltose with similar affinity before and after cross-linking (SI Appendix, Fig. S3C), suggesting that cross-linking the two residues does not significantly distort the sugar-binding site.

Crystal Structure of the Cross-Linked bcMalT EIIC.

The T280C-E54C bcMalT EIIC cross-linked by Hg²⁺ (termed bcMalT-X hereafter) can be crystallized. After extensive refinement of crystallization conditions, the crystals diffracted to a resolution of 3.2 Å, and a full dataset was collected and processed (SI Appendix, Table S1). Molecular replacement using individual interface and transport domains led to a clear solution (SI Appendix, Fig. S4 A and B). A nonprotein density is resolved at the substrate-binding site into which we can unambiguously build a maltose (SI Appendix, Fig. S4C). Since the dataset was collected at a wavelength close to the mercury edge, we calculated an anomalous difference Fourier map and it shows a strong peak (>9σ) that identifies the Hg²⁺ position between cysteines 280 and 54 (SI Appendix, Fig. S4D). The distance between the Cα atoms of cysteine 54 and 280 is 7.7 Å, and the distances between the Hg and the two sulfur atoms are ∼2.3 Å. These distances are consistent with those reported in previous crystal structures of Hg²⁺-mediated cysteine cross-links (14, 24). The final refined model contains a homodimer of bcMalT, and within each protomer, residues 5–451, one Hg²⁺ and one maltose are resolved.

When bcMalT and bcMalT-X structures were shown side-by-side with their AH1 and AH2 aligned to either side of the membrane (Fig. 2 A and B), the bound substrate on bcMalT-X is closer to the intracellular side, and its substrate-binding domain assumes an inward-facing conformation (Fig. 2A). The distance between residues 280 and 54 is smaller in the bcMalT-X structure due to the cross-linking (Fig. 2C). However, the root-mean-square deviation (rmsd) of all Cα atoms in the dimerization domain between the two structures is 0.64 Å and that of the substrate-binding domain is 0.43 Å, indicating that the cross-linking does not change the arrangement of the secondary structural elements within each domain (Fig. 2D). The structure provides direct evidence that a rigid-body elevator-type motion of the substrate-binding domain carries a substrate from one side of the membrane to another (Movie S1).

Fig. 2.

Side-by-side comparison of bcMalT and bcMalT-X. Crystal structures of bcMalT wild type (Left, PDB accession number 5IWS) and bcMalT-X (Right) are shown in cartoon (A) and surface (B) representations. In A, the two protomers are colored blue and green, respectively. Within each protomer, the dimerization domain is colored darker than the substrate-binding domain. In B, the electrostatic surface was calculated by the Adaptive Poisson–Boltzmann Solver plugin in Pymol (34); the bar represents electrostatic potential from −61.1 to +61.1 k_BT/e_C. (C) Location of T280 and E54 on a single protomer in the outward-facing conformation (Left) and inward-facing conformation (Right). TM1 is removed for clarity. C_β of T280 (magenta) and E54 (orange) are shown as spheres. (D) Superposition of the dimerization domain (Left) and substrate-binding domain (Right). Green, bcMalT wild type; blue, bcMalT-X.

Substrate-Binding Site.

Similar to the bcMalT structure, the bcMalT-X structure also has a nonprotein electron density corresponding to a bound maltose on each protomer (Fig. 3 and SI Appendix, Fig. S4C). Since there is very little change in the substrate-binding domain, the coordination of the bound maltose is essentially identical in the two structures. The C6 hydroxyl on the nonreducing end is known to be phosphorylated by EIIB, and the hydroxyl is coordinated by E355 and H240 from HP1b and TM7, respectively (Fig. 3). These two residues are implicated in the phosphotransfer reaction and are highly conserved in the glucose EIIC superfamily (25, 26) (SI Appendix, Fig. S5). The bound maltose has one additional interaction with the protein in the bcMalT-X structure. Y249 on TM7 likely forms a weak hydrogen bond with the C1 hydroxyl on the reducing end (Fig. 3). This additional hydrogen bond does not seem to affect binding affinity (SI Appendix, Fig. S3B). The distance between the hydroxyl on Y249 and the hydroxyl on the C1 is 3.1 Å in bcMalT-X and 4.5 Å in bcMalT, and the difference is due to slight movement of TM7. Coincidentally, in a previous molecular dynamics simulation study performed on the outward-facing bcMalT, Y249 and TM7 were found to be more mobile than the neighboring structural element, moving away from the substrate to open the entrance to the substrate-binding site (8).

Fig. 3.

Stereoview of the maltose-binding site in bcMalT and bcMalT-X. (A) bcMalT wild type; (B) bcMalT-X. Maltose is shown as sticks with carbon in yellow and oxygen in red. Protein–maltose interactions are marked as dotted lines between the sugar and residues from HP1 (blue), HP2 (raspberry), and TM6,7,8 (light green). The C6-OH on the nonreducing end of maltose where phosphorylation happens is marked with a star.

Major Differences Between the Inward- and Outward-Facing Structures.

The rigid-body motion of the transport domain results in different interactions between the dimerization domain and transport domain. In the previous bcMalT structure, the two domains have a buried surface area of 1,317 Å², while in the current structure of bcMalT-X the buried surface area is slightly less at 1,217 Å² (SI Appendix, Fig. S6 A and B). The buried surface is largely hydrophobic, with several hydrogen bonds. Of particular interest are residues S343 and T351 on the HP1 motif. The backbone carbonyl oxygen of A169 from the interface domain forms a hydrogen bond with the side-chain hydroxyl of S343 in the outward-facing conformation, and the same carbonyl oxygen atom forms a hydrogen bond with the hydroxyl from T351 in the inward-facing structure (SI Appendix, Fig. S6C). We also found similar exchange of hydrogen bond partners at the extracellular side, for example, K34-E397 in the outward-facing conformation and K34-N284 in the inward-facing conformation (SI Appendix, Fig. S6D). These interactions between the interface and substrate-binding domain likely stabilize the relative position of the two domains. Residues that form hydrogen bonds in the inward-facing state, S343 and T351, are both highly conserved in the glucose subfamily of EIICs such as MalT and PtsG (SI Appendix, Fig. S5). These observations also suggest that the cross-linking likely stabilizes an inward-facing state that is not significantly different from the native state.

The rigid-body motion of the substrate-binding domain is accompanied by conformational changes at both the N- and C-terminal ends of the amphipathic helix AH2 (Fig. 4). In the bcMalT outward-facing structure, AH2 becomes an extension of TM5, extending 10 Å into the extracellular space. The angle between AH2 and TM5 is 137.5°. In the bcMalT-X inward-facing structure, AH2 and TM5 forms a bend, and the angle between these two helices becomes 117.0°, and, as a result, AH2 resides horizontally at the membrane surface (Fig. 4). The bend occurs at Pro199 at the N-terminal end of AH2, which is highly conserved in the glucose subfamily of EIIs (SI Appendix, Fig. S5). This movement allows the substrate-binding domain to descend vertically toward the intracellular side. Conformational changes at the C-terminal end of AH2 are equally important for accommodating movements of the substrate-binding domain. In the bcMalT structure, six residues (215–220) at the C-terminal end of AH2 form a loop that connects TM6, and the two helices form an angle of 25°. In the bcMalT-X structure, residues S215, K216, and D217 wind into a helical turn, and the angle between AH2 and TM6 is 70° (Fig. 4). The length of AH2 changes from 17.1 Å in the outward-facing bcMalT to 20.3 Å in bcMalT-X. These changes seem to allow the rotation of the substrate-binding domain.

Fig. 4.

Conformational changes of AH2. One protomer of bcMalT (A) and bcMalT-X (B) is shown as cartoon representation. The dimerization domain is colored dark blue and the substrate-binding domain light blue. TM5 is colored green; AH2 is colored orange and TM6 is colored red. The hinge point between TM5 and AH2, P199, is marked as a magenta sphere.

Structure of bcMalT-X (T280C-E54C_Hg) Resembles the Native Inward-Facing State.

Although evidence from the cross-linking experiment suggests that the two cysteine residues are in close proximity, and hence the cross-linked bcMalT is likely not distorted into a nonnative state, we further examined the effect of cross-linking on bcMalT. We examined the stability of the bcMalT-X structure using molecular dynamics (MD) simulations. MD simulations of bcMalT-X embedded in a fully hydrated lipid bilayer showed that the structure is stable for 1 µs with or without cross-linking the two cysteines. The inward-facing conformation was well maintained in all of the simulations with backbone rmsd of 2–3 Å against the bcMalT-X crystal structure (Fig. 5A) and backbone rmsd of 7–8 Å against the outward-facing bcMalT crystal structure (Fig. 5B). The backbone rmsd of each domain is also stable, fluctuating around 1–3 Å (SI Appendix, Fig. S7 A–C). These results indicate that bcMalT-X is close to an energy minimum and likely not significantly distorted from the native conformation. In addition, we compared the bcMalT-X structure with the previous CVSMD model of bcMalT. We performed 1-µs MD simulation using the final structure from our previous bcMalT CVSMD simulation (23). The 1-µs equilibrated bcMalT CVSMD model is well aligned to the bcMalT-X structure with a backbone rmsd of 2.41 Å (SI Appendix, Fig. S7D), reinforcing the predictive power of the previous computational approach.

Fig. 5.

Backbone rmsd of bcMalT-X structure during all-atom MD simulations. (A) Average backbone rmsd between the simulated structure and bcMalT-X structure. (B) Average backbone rmsd between the simulated structure and bcMalT structure. Each line is the average of three independent simulations. Red, bcMalT-X; blue, bcMalT-X with the cross-linking between T280 and E54 removed; black, bcMalT CVSMD (23).

The proposed large motion of the substrate-binding domain would cause large distance changes between certain residues. Single-molecule Föster resonance energy transfer (smFRET) provides us a tool to visualize individual protein conformations without the need for ensemble averaging, therefore providing a method to directly observe minor protein populations that are in dynamic equilibrium. We made a mutation N288C at the extracellular side on the substrate-binding domain of bcMalT and labeled it with Alexa Fluor 488 and Alexa Fluor 594 maleimide (Fig. 6A). Similarly, M340 at the intracellular side of the substrate-binding domain was mutated and labeled with the two dyes as well. Since bcMalT is a homodimer, only the ones labeled with both dyes will register a FRET signal. The labeled proteins, when reconstituted into liposomes, transport maltose with similar efficiency as wild-type bcMalT (SI Appendix, Fig. S3D), suggesting that the mutation and the subsequent labeling do not significantly affect the motions of the protein. smFRET histograms of each mutant show two populations. For N288C, we observed one population of low FRET efficiency (E_FRET) at 0.22 and one of high E_FRET at 0.50 (Fig. 6B). The estimated distances for these two populations are 74.1 and 60.0 Å, respectively (SI Appendix, Table S2). For M340, E_FRET segregates into two well-resolved populations centered around 0.37 and 0.84 (Fig. 6C), which correspond to an estimated distance of 65.4 and 45.3 Å, respectively (SI Appendix, Table S2). As a negative control, we mutated and labeled a residue (D123) on the dimerization domain, which is predicted to remain anchored in the membrane during substrate translocation. Its E_FRET shows a uniform population at 0.59 (SI Appendix, Fig. S8), which corresponds to a distance of 56.5 Å. These distances are consistent with the two structures within the error of smFRET measurements (SI Appendix, Fig. S8 and Table S2).

Fig. 6.

smFRET on bcMalT. (A) bcMalT (Left) and bcMalT-X (Right) are shown as cartoon and colored according to Fig. 2A. C_β of N288 and M340 are shown as spheres and colored red and purple respectively. The distances between the two symmetry-related residues are marked on the dotted lines. Histograms of smFRET efficiency are shown for N288C (B) and M340C (C). Solid lines are fitting of the histograms with two Gaussian functions, and the mean value of each Gaussian function (^appE_FRET) is tabulated in SI Appendix, Table S2.

smFRET also provides an estimate to the dynamics of bcMalT (27). In both N288C and M340C, bcMalT seems to prefer the outward- to the inward-facing conformation by a ratio of 5:1 and 7:3, respectively. This fractional population ratio corresponds to a free energy difference of approximately 2–4 kJ/mol. Similar energy difference was observed in conformational changes of Glt_ph measured by the atomic force microscopy (28). A more stable outward-facing conformation seems consistent with a slightly more extensive buried interface between the dimerization and substrate-binding domains and may explain why it was difficult to crystallize the wild-type bcMalT in an inward-facing conformation.

Summary and Discussion

The structures of bcMalT and bcMalT-X provide direct visualization of the outward- and inward-facing conformations of an EIIC from the glucose superfamily (Fig. 2A and Movie S1). The structures show that the substrate-binding domain moves as a rigid body that keeps the substrate-binding site intact while moving it to face the alternate side of the membrane. An amphipathic helix, AH2, which connects the dimerization and the substrate-binding domains, bends at a conserved hinge point and changes its length to accommodate the movement of the substrate-binding domain.

The bcMalT-X structure shows that the substrate-binding domain has a 9-Å vertical translation and a 45° rotation. Such large-scale motions are common among transporters using the elevator-type mechanism (14 ⇓⇓⇓⇓⇓⇓⇓–22). In at least three of the multimeric transporters that have an elevator-type mechanism, the substrate-binding domains can move independently of each other. Both smFRET and atomic force microscopy studies have visualized the unsynchronized subunit motion in a single trimeric Glt_ph (19, 28). In crystal structures of CNT_NW, one transport domain of the trimeric transporter was found in different states than the other two (20). In addition, the structure of sodium citrate symporter SeCitS captured an asymmetric state of the dimer, with one protomer in the outward-facing state and the other in the inward-facing state (22). It is not clear whether in bcMalT the two substrate-binding domains can move independently. If there exists a conformation in bcMalT where one protomer is outward-facing and the other inward-facing, a population of E_FRET at 0.34 for N288 and 0.63 for M340 would be expected on the smFRET histogram. However, we were not able to resolve either of these states under the current experimental conditions.

The substrate in bcMalT-X is now accessible to solvent from the cytoplasm. Among six independent MD simulations, we have observed two sugar release events: one in the bcMalT CVSMD system and the other in the bcMalT-X without the disulfide bond system (SI Appendix, Fig. S9A). The sugar molecules were released without any significant conformational change during the simulations, suggesting that the bcMalT-X structure has an inward-facing open conformation. The comparison of the bcMalT-X with bcChbC (inward-occluded) crystal structures also supports this observation, as the intracellular exit of the sugar-binding site is blocked by the TM4-5 loop in bcChbC, while the same loop has a different orientation in bcMalT-X and no longer covers the sugar-binding site (SI Appendix, Fig. S9 B and C). Thus, bcMalT-X structure likely represents a conformation that is compatible for phosphate transfer from the EIIB. These observations also provide an explanation for facilitated sugar transport activity of bcMalT when no phosphorylation occurs.

In summary, the combined approach of structural biology, MD simulations, and smFRET revealed conformational changes required for substrate translocation in an elevator-type mechanism of transport. The inward-facing open conformation also provides a starting point for understanding how EIIB could interact with EIIC and how a phosphate group is transferred to the bound maltose.

Methods

Detailed materials and methods are found in SI Appendix. Protein purification and cross-linking experiments followed established protocols reported previously (8, 23). bcMalT-X was crystallized using the sitting-drop vapor diffusion method. The dataset was collected close to the mercury edge, and the phase problem was solved by molecular replacement. Maltose binding and transport were measured using the scintillation proximity assay and liposome uptake assay, respectively, as described previously (8, 23). MD simulations were conducted in CHARMM-GUI (29, 30), following optimized protocols (31, 32). For smFRET experiments, labeling conditions were optimized to maximize the amount of protein that contained both dyes. Diffusion-based smFRET was conducted using a custom-built ISS Alba confocal laser microscopy system, as described previously (33).

Acknowledgments

We thank K. Rajashankar for advice on X-ray crystallography and K. Rajashankar, L. Keefe, E. Zoellner, K. Battaile, and A. Mulichak for beamline support. We thank R. Bruni and B. Kloss, both from the Center on Membrane Protein Production and Analysis in New York City, for the cloning and initial screen of EIIC genes. This work was supported by National Key Basic Research Program of China 2014CB910301 (to M.Z.); National Institutes of Health Grants U54GM087519 (to W.I. and M.Z.) and GM098878, DK088057, and HL086392 (to M.Z.); and Grant 12EIA8850017 from the American Heart Association and Cancer Prevention and Research Institute of Texas Grant R12MZ (both to M.Z.).

Footnotes

↵¹Z.R. and J.L. contributed equally to this work.
↵²To whom correspondence may be addressed. Email: mzhou{at}bcm.edu, allan.ferreon{at}bcm.edu, or woi216{at}lehigh.edu.

Author contributions: Z.R., J.L., M.M.M., Y.N., L.H., Z.X., J.G.M., A.C.M.F., W.I., and M.Z. designed research, collected and analyzed data, and wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.wwpdb.org (PDB ID code 6BVG).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1800647115/-/DCSupplemental.

Published under the PNAS license.

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(2009) Transport mechanism of a bacterial homologue of glutamate transporters. Nature 462:880–885.
OpenUrl CrossRef PubMed
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1. Canul-Tec JC, et al.
(2017) Structure and allosteric inhibition of excitatory amino acid transporter 1. Nature 544:446–451.
OpenUrl CrossRef PubMed
↵
1. Yernool D,
2. Boudker O,
3. Jin Y,
4. Gouaux E
(2004) Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature 431:811–818.
OpenUrl CrossRef PubMed
↵
1. Zhou X, et al.
(2014) Structural basis of the alternating-access mechanism in a bile acid transporter. Nature 505:569–573.
OpenUrl CrossRef PubMed
↵
1. Lee C, et al.
(2013) A two-domain elevator mechanism for sodium/proton antiport. Nature 501:573–577.
OpenUrl CrossRef PubMed
↵
1. Erkens GB,
2. Hänelt I,
3. Goudsmits JMH,
4. Slotboom DJ,
5. van Oijen AM
(2013) Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters. Nature 502:119–123.
OpenUrl CrossRef PubMed
↵
1. Hirschi M,
2. Johnson ZL,
3. Lee SY
(2017) Visualizing multistep elevator-like transitions of a nucleoside transporter. Nature 545:66–70.
OpenUrl
↵
1. Mancusso R,
2. Gregorio GG,
3. Liu Q,
4. Wang D-N
(2012) Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter. Nature 491:622–626.
OpenUrl CrossRef PubMed
↵
1. Wöhlert D,
2. Grötzinger MJ,
3. Kühlbrandt W,
4. Yildiz Ö
(2015) Mechanism of Na(+)-dependent citrate transport from the structure of an asymmetrical CitS dimer. eLife 4:e09375.
OpenUrl CrossRef
↵
1. Lee J,
2. Ren Z,
3. Zhou M,
4. Im W
(2017) Molecular simulation and biochemical studies support an elevator-type transport mechanism in EIIC. Biophys J 112:2249–2252.
OpenUrl
↵
1. Verdon G,
2. Oh S,
3. Serio RN,
4. Boudker O
(2014) Coupled ion binding and structural transitions along the transport cycle of glutamate transporters. eLife 3:e02283.
OpenUrl CrossRef PubMed
↵
1. Saraceni-Richards CA,
2. Jacobson GR
(1997) A conserved glutamate residue, Glu-257, is important for substrate binding and transport by the Escherichia coli mannitol permease. J Bacteriol 179:1135–1142.
OpenUrl Abstract/FREE Full Text
↵
1. Ruijter GJ,
2. van Meurs G,
3. Verwey MA,
4. Postma PW,
5. van Dam K
(1992) Analysis of mutations that uncouple transport from phosphorylation in enzyme IIGlc of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system. J Bacteriol 174:2843–2850.
OpenUrl Abstract/FREE Full Text
↵
1. Ferreon ACM,
2. Ferreon JC,
3. Wright PE,
4. Deniz AA
(2013) Modulation of allostery by protein intrinsic disorder. Nature 498:390–394.
OpenUrl CrossRef PubMed
↵
1. Ruan Y, et al.
(2017) Direct visualization of glutamate transporter elevator mechanism by high-speed AFM. Proc Natl Acad Sci USA 114:1584–1588.
OpenUrl Abstract/FREE Full Text
↵
1. Jo S,
2. Kim T,
3. Iyer VG,
4. Im W
(2008) CHARMM-GUI: A web-based graphical user interface for CHARMM. J Comput Chem 29:1859–1865.
OpenUrl CrossRef PubMed
↵
1. Lee J, et al.
(2016) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J Chem Theory Comput 12:405–413.
OpenUrl CrossRef PubMed
↵
1. Wu EL, et al.
(2014) CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem 35:1997–2004.
OpenUrl CrossRef PubMed
↵
1. Jo S,
2. Lim JB,
3. Klauda JB,
4. Im W
(2009) CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J 97:50–58.
OpenUrl CrossRef PubMed
↵
1. Tsoi PS, et al.
(2017) The N-terminal domain of ALS-linked TDP-43 assembles without misfolding. Angew Chem Int Ed Engl 56:12590–12593.
OpenUrl CrossRef PubMed
↵
1. Baker NA,
2. Sept D,
3. Joseph S,
4. Holst MJ,
5. McCammon JA
(2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037–10041.
OpenUrl Abstract/FREE Full Text

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Proceedings of the National Academy of Sciences: 115 (23)

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Article Classifications

Biological Sciences
Biochemistry

[1] ↵
Kaback HR
(1968) The role of the phosphoenolpyruvate-phosphotransferase system in the transport of sugars by isolated membrane preparations of Escherichia coli. J Biol Chem 243:3711–3724.
OpenUrl Abstract/FREE Full Text

[2] Kaback HR

[3] ↵
Deutscher J, et al.
(2014) The bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system: Regulation by protein phosphorylation and phosphorylation-dependent protein-protein interactions. Microbiol Mol Biol Rev 78:231–256.
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[4] Deutscher J, et al.

[5] ↵
Kundig W,
Ghosh S,
Roseman S
(1964) Phosphate bound to histidine in a protein as an intermediate in a novel phospho-transferase system. Proc Natl Acad Sci USA 52:1067–1074.
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[6] Kundig W,

[7] Ghosh S,

[8] Roseman S

[9] ↵
Kundig W,
Kundig FD,
Anderson B,
Roseman S
(1966) Restoration of active transport of glycosides in Escherichia coli by a component of a phosphotransferase system. J Biol Chem 241:3243–3246.
OpenUrl Abstract/FREE Full Text

[10] Kundig W,

[11] Kundig FD,

[12] Anderson B,

[13] Roseman S

[14] ↵
McCoy JG,
Levin EJ,
Zhou M
(2015) Structural insight into the PTS sugar transporter EIIC. Biochim Biophys Acta 1850:577–585.
OpenUrl CrossRef

[15] McCoy JG,

[16] Levin EJ,

[17] Zhou M

[18] ↵
Saier MH,
Hvorup RN,
Barabote RD
(2005) Evolution of the bacterial phosphotransferase system: From carriers and enzymes to group translocators. Biochem Soc Trans 33:220–224.
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[19] Saier MH,

[20] Hvorup RN,

[21] Barabote RD

[22] ↵
Cao Y, et al.
(2011) Crystal structure of a phosphorylation-coupled saccharide transporter. Nature 473:50–54.
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[23] Cao Y, et al.

[24] ↵
McCoy JG, et al.
(2016) The structure of a sugar transporter of the glucose EIIC superfamily provides insight into the elevator mechanism of membrane transport. Structure 24:956–964.
OpenUrl CrossRef

[25] McCoy JG, et al.

[26] ↵
Luo P, et al.
(2015) Crystal structure of a phosphorylation-coupled vitamin C transporter. Nat Struct Mol Biol 22:238–241.
OpenUrl

[27] Luo P, et al.

[28] ↵
Jeckelmann J-M, et al.
(2011) Structure and function of the glucose PTS transporter from Escherichia coli. J Struct Biol 176:395–403.
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[29] Jeckelmann J-M, et al.

[30] ↵
Koning RI, et al.
(1999) The 5 Å projection structure of the transmembrane domain of the mannitol transporter enzyme II. J Mol Biol 287:845–851.
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[31] Koning RI, et al.

[32] ↵
Kalbermatter D, et al.
(2017) Electron crystallography reveals that substrate release from the PTS IIC glucose transporter is coupled to a subtle conformational change. J Struct Biol 199:39–45.
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[33] Kalbermatter D, et al.

[34] ↵
Mitchell P
(1957) A general theory of membrane transport from studies of bacteria. Nature 180:134–136.
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[35] Mitchell P

[36] ↵
Reyes N,
Ginter C,
Boudker O
(2009) Transport mechanism of a bacterial homologue of glutamate transporters. Nature 462:880–885.
OpenUrl CrossRef PubMed

[37] Reyes N,

[38] Ginter C,

[39] Boudker O

[40] ↵
Canul-Tec JC, et al.
(2017) Structure and allosteric inhibition of excitatory amino acid transporter 1. Nature 544:446–451.
OpenUrl CrossRef PubMed

[41] Canul-Tec JC, et al.

[42] ↵
Yernool D,
Boudker O,
Jin Y,
Gouaux E
(2004) Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature 431:811–818.
OpenUrl CrossRef PubMed

[43] Yernool D,

[44] Boudker O,

[45] Jin Y,

[46] Gouaux E

[47] ↵
Zhou X, et al.
(2014) Structural basis of the alternating-access mechanism in a bile acid transporter. Nature 505:569–573.
OpenUrl CrossRef PubMed

[48] Zhou X, et al.

[49] ↵
Lee C, et al.
(2013) A two-domain elevator mechanism for sodium/proton antiport. Nature 501:573–577.
OpenUrl CrossRef PubMed

[50] Lee C, et al.

[51] ↵
Erkens GB,
Hänelt I,
Goudsmits JMH,
Slotboom DJ,
van Oijen AM
(2013) Unsynchronised subunit motion in single trimeric sodium-coupled aspartate transporters. Nature 502:119–123.
OpenUrl CrossRef PubMed

[52] Erkens GB,

[53] Hänelt I,

[54] Goudsmits JMH,

[55] Slotboom DJ,

[56] van Oijen AM

[57] ↵
Hirschi M,
Johnson ZL,
Lee SY
(2017) Visualizing multistep elevator-like transitions of a nucleoside transporter. Nature 545:66–70.
OpenUrl

[58] Hirschi M,

[59] Johnson ZL,

[60] Lee SY

[61] ↵
Mancusso R,
Gregorio GG,
Liu Q,
Wang D-N
(2012) Structure and mechanism of a bacterial sodium-dependent dicarboxylate transporter. Nature 491:622–626.
OpenUrl CrossRef PubMed

[62] Mancusso R,

[63] Gregorio GG,

[64] Liu Q,

[65] Wang D-N

[66] ↵
Wöhlert D,
Grötzinger MJ,
Kühlbrandt W,
Yildiz Ö
(2015) Mechanism of Na(+)-dependent citrate transport from the structure of an asymmetrical CitS dimer. eLife 4:e09375.
OpenUrl CrossRef

[67] Wöhlert D,

[68] Grötzinger MJ,

[69] Kühlbrandt W,

[70] Yildiz Ö

[71] ↵
Lee J,
Ren Z,
Zhou M,
Im W
(2017) Molecular simulation and biochemical studies support an elevator-type transport mechanism in EIIC. Biophys J 112:2249–2252.
OpenUrl

[72] Lee J,

[73] Ren Z,

[74] Zhou M,

[75] Im W

[76] ↵
Verdon G,
Oh S,
Serio RN,
Boudker O
(2014) Coupled ion binding and structural transitions along the transport cycle of glutamate transporters. eLife 3:e02283.
OpenUrl CrossRef PubMed

[77] Verdon G,

[78] Oh S,

[79] Serio RN,

[80] Boudker O

[81] ↵
Saraceni-Richards CA,
Jacobson GR
(1997) A conserved glutamate residue, Glu-257, is important for substrate binding and transport by the Escherichia coli mannitol permease. J Bacteriol 179:1135–1142.
OpenUrl Abstract/FREE Full Text

[82] Saraceni-Richards CA,

[83] Jacobson GR

[84] ↵
Ruijter GJ,
van Meurs G,
Verwey MA,
Postma PW,
van Dam K
(1992) Analysis of mutations that uncouple transport from phosphorylation in enzyme IIGlc of the Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system. J Bacteriol 174:2843–2850.
OpenUrl Abstract/FREE Full Text

[85] Ruijter GJ,

[86] van Meurs G,

[87] Verwey MA,

[88] Postma PW,

[89] van Dam K

[90] ↵
Ferreon ACM,
Ferreon JC,
Wright PE,
Deniz AA
(2013) Modulation of allostery by protein intrinsic disorder. Nature 498:390–394.
OpenUrl CrossRef PubMed

[91] Ferreon ACM,

[92] Ferreon JC,

[93] Wright PE,

[94] Deniz AA

[95] ↵
Ruan Y, et al.
(2017) Direct visualization of glutamate transporter elevator mechanism by high-speed AFM. Proc Natl Acad Sci USA 114:1584–1588.
OpenUrl Abstract/FREE Full Text

[96] Ruan Y, et al.

[97] ↵
Jo S,
Kim T,
Iyer VG,
Im W
(2008) CHARMM-GUI: A web-based graphical user interface for CHARMM. J Comput Chem 29:1859–1865.
OpenUrl CrossRef PubMed

[98] Jo S,

[99] Kim T,

[100] Iyer VG,

[101] Im W

[102] ↵
Lee J, et al.
(2016) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J Chem Theory Comput 12:405–413.
OpenUrl CrossRef PubMed

[103] Lee J, et al.

[104] ↵
Wu EL, et al.
(2014) CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem 35:1997–2004.
OpenUrl CrossRef PubMed

[105] Wu EL, et al.

[106] ↵
Jo S,
Lim JB,
Klauda JB,
Im W
(2009) CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J 97:50–58.
OpenUrl CrossRef PubMed

[107] Jo S,

[108] Lim JB,

[109] Klauda JB,

[110] Im W

[111] ↵
Tsoi PS, et al.
(2017) The N-terminal domain of ALS-linked TDP-43 assembles without misfolding. Angew Chem Int Ed Engl 56:12590–12593.
OpenUrl CrossRef PubMed

[112] Tsoi PS, et al.

[113] ↵
Baker NA,
Sept D,
Joseph S,
Holst MJ,
McCammon JA
(2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037–10041.
OpenUrl Abstract/FREE Full Text

[114] Baker NA,

[115] Sept D,

[116] Joseph S,

[117] Holst MJ,

[118] McCammon JA

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Structure of an EIIC sugar transporter trapped in an inward-facing conformation

Significance

Abstract

Results

Trapping bcMalT in an Inward-Facing Conformation.

Crystal Structure of the Cross-Linked bcMalT EIIC.

Substrate-Binding Site.

Major Differences Between the Inward- and Outward-Facing Structures.

Structure of bcMalT-X (T280C-E54C_Hg) Resembles the Native Inward-Facing State.

Summary and Discussion

Methods

Acknowledgments

Footnotes

References

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Structure of an EIIC sugar transporter trapped in an inward-facing conformation

Significance

Abstract

Results

Trapping bcMalT in an Inward-Facing Conformation.

Crystal Structure of the Cross-Linked bcMalT EIIC.

Substrate-Binding Site.

Major Differences Between the Inward- and Outward-Facing Structures.

Structure of bcMalT-X (T280C-E54CHg) Resembles the Native Inward-Facing State.

Summary and Discussion

Methods

Acknowledgments

Footnotes

References

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Structure of bcMalT-X (T280C-E54C_Hg) Resembles the Native Inward-Facing State.