The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 Å resolution

Crystal structure of RlmA I : Implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site

“…4). Manual docking of the portion of the E. coli rRNA structure containing hairpins 33, 34, and 35 (nucleotides 692-770) (37), into the RNA-binding cleft of RlmA I provides a unique complementary match (Fig. 5A).…”

“…Docking of the rRNA substrate predicts that regions 6-8, 25, 38-52, 117-119, 138-141, 157-162, and 233-235 of molecule 1 and 6-8, 25, 38-52, 115-121, and 136-140 of molecule 2 of the RlmA I dimer are likely to be involved in protein͞RNA interactions. The length of the polypeptide linker (amino acids [35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52] between the two domains is 3-4 aa shorter in RlmA II than in RlmA I (Fig. 1 A).…”

“…Amino acid sequence comparison of RlmA I and RlmA II and mapping of the conserved regions onto the crystal structure of E. coli RlmA I indicate positioning of some of the key conserved amino acid residues at putative RNA-binding regions, at the SAM-binding pocket, and at the dimer interface. Docking the publicly available atomic coordinates for hairpin 35 of 23S rRNA and surrounding regions (3,5,(37)(38)(39) into the cleft of RlmA I dimer shows complementary RNA͞protein structural features. This crystal structure, along with earlier reported biochemical data, provides a basis for detailed investigations aimed at understanding structural features of the specific recognition of rRNA substrates, the role of this type of Zn-finger in RNA recognition, general aspects of RNA͞protein interactions, and the mechanism of RNA methylation by RlmA enzymes.…”

The function of lexical motifs in the organization of the Actinomycetes 5S rRNAs

“…The main binding sites of E. coli 5S RNA, the rpL5 and rpL18 proteins, are found in these domains with the hinge region conformation being critical for the initial recognition of rpL18 (9,10,14,18,23,24,34). Such a configuration seems to guarantee the conformation stability necessary for recognition.…”

“…Some studies have adopted an alternative tertiary conformation for the E. coli 5S RNA, based on interaction between C38 and U40 and the rpL5 ribosomal protein (14). However, the presence of this triplet in the same 23S fragment, where GGR triplets are found, points to a potential rpL18 protein receptor, which serves as a functional motif analogue to GGR triplets.…”