Proteopedia entry: The large ribosomal subunit of Haloarcula marismortui

This Proteopedia page presents the refined version of the structure of the Haloarcula large ribosomal subunit as solved by the laboratories of Thomas Steitz and Peter Moore. The landmark structure (Fig, 1, left) is of great impact as it is the first atomic-resolution structure of the highly conserved ribosomal subunit which harbors peptide bond-forming activity; it served as the basis for which Thomas Steitz shared the 2009 Nobel Prize in Chemistry with Venkatraman Ramakrishnan and Ada Yonath. The structural data includes 27 proteins and over 3000 nucleotides of RNA. Visitors can control the display of the general features using toggles below the scene windows. The key highlights revealed as visitors explore the scenes: (a) Protein is in the minority compared to RNA in the ribosomal subunit. (b) Only half the proteins seen in the large subunit are typical globular proteins; the other half are extended or have significant extended regions that fill gaps in between the RNA. (c) The structural data includes an analog that corresponds to portions of multiple substrates as observed during an intermediate state of peptide bond formation, and the bound position of the analog relative to the ribosomal proteins clearly demonstrates the stunning revelation that protein does not play a direct role in the chemistry of peptide bond synthesis by the ribosome (Fig. 1, right). (d) A prominent tunnel that would accommodate the growing polypeptide chain and permit its extrusion from the subunit can readily be observed extending from the point at which the multisubstrate analog binds back through the entire subunit. The large ribosomal subunit topic page in Proteopedia presents the large ribosomal subunit seen here (left) along with a multisubstrate analog (magenta) bound. On the right, an interactive scene on the page highlights the region boxed in red on the left and clearly illustrates how no amino acids are significantly close enough to contribute to the chemistry at the site of peptide bond formation (yellow). Link: http: //www. proteopedia. org/wiki/index. php/LargeRibosomalSubunitₒfHaloarcula