1M90
Co-crystal structure of CCA-Phe-caproic acid-biotin and sparsomycin bound to the 50S ribosomal subunit
Summary for 1M90
| Entry DOI | 10.2210/pdb1m90/pdb |
| Related | 1FFZ 1FGO 1JJ2 1K73 1KC8 1KQS |
| Descriptor | 23S RRNA, RIBOSOMAL PROTEIN L10, RIBOSOMAL PROTEIN L10E, ... (40 entities in total) |
| Functional Keywords | p-site, sparsomycin, ribosome |
| Biological source | Haloarcula marismortui More |
| Cellular location | Cytoplasm : P12743 |
| Total number of polymer chains | 31 |
| Total formula weight | 1459740.21 |
| Authors | Hansen, J.L.,Schmeing, T.M.,Moore, P.B.,Steitz, T.A. (deposition date: 2002-07-26, release date: 2002-09-06, Last modification date: 2023-11-15) |
| 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 Cited by 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: 12185246DOI: 10.1073/pnas.172404099 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.8 Å) |
Structure validation
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