Cryo-EM structure of the polyphosphate polymerase VTC: Coupling polymer synthesis to membrane transit

The eukaryotic polyphosphate (polyP) polymerase VTC complex synthesizes polyP from adenosine triphosphate (ATP) and translocates polyP across the vacuolar membrane to maintain an intracellular phosphate (Pi) homeostasis. To discover how VTC complex solves this fundamental aspect, we determined a cryo-electron microscopy structure of an endogenous VTC complex (Vtc4/Vtc3/Vtc1) from Saccharomyces cerevisiae at 3.1 [A] resolution. The structure reveals a heteropentameric architecture of one Vtc4, one Vtc3 and three Vtc1 subunits. The transmembrane region forms a polyP selective channel, probably adopting a resting state conformation, in which a latch-like, horizonal helix of Vtc4 limits the entrance. The catalytic Vtc4 central domain locates on top of the pseudo-symmetric polyP channel, creating a strongly electropositive pathway for nascent polyP that can couple synthesis to translocation. The SPX domain of Vtc4 positively regulates polyP synthesis and regulation of VTC complex. The non-catalytic Vtc3 regulates VTC through a phoshorylatable loop. Our findings, along with the functional data, allow us to propose a mechanism of polyP channel gating and VTC complex activation.