Cryo-EM studies of the fourE. coliparalogs establish ABCF proteins as master plumbers of the peptidyl-transferase center of the ribosome

Author:

Singh ShikhaORCID,Gentry Riley C.,Fu Ziao,Bailey Nevette A.,Altomare Clara G.,Wong Kam-Ho,Neky Matthew J.,Wang ChiORCID,Ray Korak KumarORCID,Chi Ying-Chih,Zhang Zhening,Grassucci Robert A.,Frank Joachim,Boël Grégory,Gonzalez Ruben L.ORCID,Hunt John F.ORCID

Abstract

The genomes of most mesophilic organisms encode multipleATP-BindingCassetteF(ABCF) proteins. EttA, one of fourE. coliparalogs, regulates synthesis of the first peptide bond on the ribosome dependent on ATP/ADP ratio, whileAntibioticResistance factors (AREs), paralogs in other organisms, both regulate and directly mediate resistance to ribosome-targeted antibiotics. However, the physiological functions remain unclear for most paralogs, and the mechanism-of-action has yet to be rigorously established for any paralog. We herein present single particle cryogenic electron microscopy structures of ribosome complexes of all fourE. coliABCF paralogs (EttA, Uup, YbiT, and YheS), which, together with previously determined ARE structures, show that ABCFs control the binding geometry of the tRNA in the peptidyl-tRNA-binding (P) site on the ribosome. They modulate the position of its acceptor stem relative to the peptidyl transferase center (PTC) in a manner that can either promote (EttA and Uup) or disrupt (YbiT, YheS, and the AREs) proper catalytic geometry. The YbiT/70S reconstructions include a conformation with no density for ribosomal protein bL33, and structural analyses support the exchange of this sub-stoichiometric ribosomal protein being functionally related to conformational changes in YbiT controlled by sequence variations in the strongly non-canonical Signature Sequence in its first ABC domain. Our studies establish general structural/enzymological principles by which the ATPase activity of ABCF proteins controls translation elongation coupled to modulation of conformation and stereochemistry in the catalytic core of the ribosome.

Publisher

Cold Spring Harbor Laboratory

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