KdpFABC is an oligomeric K
+ transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K
+ transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases. Recent structural work has defined the architecture and generated contradictory hypotheses for the transport mechanism. Here, we use substrate analogs to stabilize four key intermediates in the reaction cycle and determine the corresponding structures by cryogenic electron microscopy. We find that KdpB undergoes conformational changes consistent with other representatives from the P-type superfamily, whereas KdpA, KdpC, and KdpF remain static. We observe a series of spherical densities that we assign as K
+ or water and which define a pathway for K
+ transport. This pathway runs through an intramembrane tunnel in KdpA and delivers ions to sites in the membrane domain of KdpB. Our structures suggest a mechanism where ATP hydrolysis is coupled to K
+ transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K
+ to the cytoplasm.KdpFABC is an ATP-dependent K
+ pump in prokaryotes, essential for osmoregulation in K
+-deficient environments. Expression of kdpFABC is induced when external K
+ concentrations fall into the micromolar range, where constitutive K
+-uptake systems, Trk and Kup, can no longer maintain intracellular K
+ levels. Under these conditions, a high-affinity active transport system is required to maintain internal concentrations of K
+, essential for regulating pH, membrane potential, and the turgor pressure that drives cell growth and division (
1). As a molecular machine, the oligomeric KdpFABC complex represents a fascinating hybrid that couples a channel-like subunit (KdpA)—related to the superfamily of K
+ transporters (SKT)—with a pump-like subunit (KdpB)—belonging to the superfamily of P-type ATPases (
2). Early studies established a role for KdpA in the selectivity and transport of K
+ (
3). Furthermore, analysis of KdpA sequence and topology established the existence of four approximate repeats of the “MPM” fold that characterizes K
+ channels and a close resemblance to bacterial potassium channels TrkH and KtrB (
4). KdpB, on the other hand, harnesses the energy of ATP to drive transport of K
+ against a concentration gradient. KdpB was shown to employ the Post–Albers reaction scheme (
5) that features two main conformational states, E1 and E2, and an aspartyl phosphate intermediate (). However, mechanisms for coupling between these two subunits have remained elusive, as has the specific transport pathway of K
+ through the complex (
6).
Open in a separate windowOverview of cryo-EM structures. (
A) Cryo-EM density maps of KdpFABC in four unique conformational states, corresponding to intermediates in the Post–Albers reaction cycle. KdpA is green; KdpB is brown, blue, yellow, and red; KdpC is purple; and KdpF is cyan. (
B) Close-up of catalytic sites in which density is clearly visible for AMP-PCP and MgF
4; lower resolution of the E2-P map makes explicit placement of BeF
3 ambiguous. Mg
2+ ions are green, and protein domains are colored as in
A.Recent structural studies have generated renewed interest in KdpFABC and have led to new and conflicting ideas about its transport process. The first structure was determined by X-ray crystallography, defining the architecture of the complex (
7). This structure revealed a sperical density modeled as water bound at the unwound part of the M4 transmembrane helix of KdpB (
SI Appendix, Fig. S1A). This site, here denoted Bx, is conserved among P-type ATPases and plays a key role in binding and transporting their respective substrates. Structures of the well-studied sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) revealed ions at two sites, dubbed site Ca(I) and site Ca(II), the latter of which is congruent with the Bx site in KdpB. Structures of Na,K-ATPase show a similar ion binding pattern, with a third Na
+ ion also accommodated near these two conserved sites. In KdpA, a K
+ ion was bound within the selectivity filter (SF) and, like TrkH and KtrB, the third MPM repeat featured a kinked helix (D3M
2 in
SI Appendix, Fig. S1A) with a loop that blocks this ion from traveling across the membrane. This loop was suggested to function as a gate that would move aside to open a pore for transport. In addition, a 40-Å–long tunnel was seen encapsulated within the membrane domain of KdpFABC. This intramembrane tunnel connects the SF in KdpA with the Bx site in KdpB, leading to a proposal for energy coupling based on a Grothuss mechanism for charge transfer between these sites. According to this mechanism, the tunnel is filled with water molecules acting as a water wire to shuttle protons between the subunits. K
+ binding to the SF would initiate proton hopping through the tunnel. Arrival of this charge at the Bx site would stimulate the cycle of ATP hydrolysis, as documented in other P-type ATPases. A salt-bridge network connecting cytoplasmic loops of KdpA and KdpB would then tug on the kinked D3M
2 helix in KdpA, thus displacing the gating loop and allowing K
+ to transit the membrane.Two additional structures of KdpFABC were subsequently determined by cryogenic electron microscopy (cryo-EM), revealing two additional conformations (
8). Whereas the crystal structure appeared to represent an inhibited conformation due to the influence of serine phosphorylation (
9), these cryo-EM structures were compatible with E1 and E2 states. The intramembrane tunnel was intact in the E1 state but was interrupted in the E2 state due to conformational changes in KdpB. These observations led to the proposal of an alternative mechanism in which K
+ ions move through the tunnel, from the SF of KdpA to the Bx site of KdpB, where they are released to the cytoplasm at the appropriate step in the reaction cycle. The other two subunits, KdpC and KdpF, were also observed in all of these structures. KdpF consists of a single transmembrane helix at the interface of KdpA and KdpB, possibly serving to stabilize the complex. KdpC has a unique periplasmic domain anchored by a single TM helix; the location at the entrance to the SF suggested that this domain might act as a periplasmic filter or gate, though evidence for this role is currently lacking.To shed more light on the coupling between KdpA and KdpB and to resolve the role of the intramembrane tunnel, we determined structures of the KdpFABC complex in all of the major enzymatic states. We used inhibitors to trap the complex in various discrete states, in the presence of either K
+ or Na
+, and imaged these samples by cryo-EM. In this way, we produced 14 independent density maps at resolutions between 2.9 and 3.7 Å; four of these were selected to represent the primary intermediates from the reaction cycle. These resulting structures display significant conformational changes in KdpB as well as nonprotein spherical densities within the SF of KdpA, within the intramembrane tunnel, and in KdpB near the Bx site. In contrast, KdpA is static suggesting that it serves simply to select K
+ ions from the periplasm and shuttle them to transport sites in KdpB. By providing high-resolution detail to structural changes in these sites during the reaction cycle, we provide evidence and a comprehensive model for the transport mechanism in which K
+ from the periplasm enters the SF of KdpA, moves through the tunnel to the Bx site, and is released to the cytoplasm by KdpB.
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