23S ribosomal RNA
The 23S rRNA is a 2,904 nucleotide long (in E. coli) component of the large subunit (50S) of the bacterial/archean ribosome and makes up the peptidyl transferase center (PTC).[2] The 23S rRNA is divided into six secondary structural domains titled I-VI, with the corresponding 5S rRNA being considered domain VII.[3] The ribosomal peptidyl transferase activity resides in domain V of this rRNA, which is also the most common binding site for antibiotics that inhibit translation, making it a target for ribosomal engineering.[2] A well-known member of this antibiotic class, chloramphenicol, acts by inhibiting peptide bond formation, with recent 3D-structural studies showing two different binding sites depending on the species of ribosome. Numerous mutations in domains of the 23S rRNA with Peptidyl transferase activity have resulted in antibiotic resistance.[4] 23S rRNA genes typically have higher sequence variations, including insertions and/or deletions, compared to other rRNAs.[5]
23S and 5S ribosomal RNAs
The eukaryotic homolog of the 23S LSU rRNA is the 28S ribosomal RNA, with a region filled by the 5.8S ribosomal RNA.[6]
23S rRNA Helix 26a[edit]
The 23S ribosomal RNA is composed of six domains forming a complex network of molecular interactions. A central single-stranded region connects all of the domains through base-pairing of the two halves, forming Helix 26a. Some consider Helix 26a to be Domain 0 due to its action as a central core and compact folding unit. Comparison of 23S and 28S ribosomal RNA sequences across species demonstrate conservation of Helix 26a. Helices continue to provide the support as the backbone of domain architecture.[9]
Plastid[edit]
Chloroplast ribosomes from "higher" plants have an additional 4.5S rRNA created by fragmentation of 23S. It is located to the 3' side of 23S in the rRNA operon and corresponds to the 3' end of non-fragmented 23S rRNA.[10]