Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle

The signal recognition particle (SRP) is a ribonucleoprotein complex respon sible for targeting proteins to the endoplasmic reticulum in eukarya or to the inner membrane in prokarya. The crystal structure of the universally co nserved RNA-protein core of the Escherichia coli SRP, refined here to 1.5 A ngstrom resolution, revealed minor groove recognition of the 4.5 S RNA comp onent by the M domain of the Ffh protein. Within the RNA, nucleotides compr ising two phylogenetically conserved internal loops create a unique surface for protein recognition. To determine the energetic importance of conserve d nucleotides for SRP assembly, we measured the affinity of the M domain fo r a series of RNA mutants. This analysis reveals how conserved nucleotides within the two internal loop motifs establish the architecture of the macro molecular interface and position essential functional groups for direct rec ognition by the protein. (C) 2001 Academic Press.