1Q86

Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.

Summary for 1Q86

• Entry DOI: 10.2210/pdb1q86/pdb
• Related: 1KQS 1M90 1Q7Y 1Q81 1Q82
• Descriptor: 23S ribosomal rna, Acidic ribosomal protein P0 homolog, L10 Ribosomal Protein, ... (38 entities in total)
• Functional Keywords: ribosome 50s, a-site, p-site, protein-protein complex, rna-rna complex, protein-rna complex, ribosome
• Biological source: Haloarcula marismortui; More
• Cellular location: Cytoplasm : P12743
• Total number of polymer chains: 32
• Total formula weight: 1460267.10

Authors

Hansen, J.L.,Schmeing, T.M.,Moore, P.B.,Steitz, T.A. (deposition date: 2003-08-20, release date: 2003-10-07, Last modification date: 2023-08-16)

Primary citation

Hansen, J.L.,Schmeing, T.M.,Moore, P.B.,Steitz, T.A.
Structural insights into peptide bond formation.
Proc.Natl.Acad.Sci.USA, 99:11670-11675, 2002

PubMed Abstract: The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.

PubMed: 12185246
DOI: 10.1073/pnas.172404099

Experimental method

X-RAY DIFFRACTION (3 Å)