5DM6

Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans

Summary for 5DM6

• Entry DOI: 10.2210/pdb5dm6/pdb
• Descriptor: 50S ribosomal protein L1, 50S ribosomal protein L15, 50S ribosomal protein L16, ... (31 entities in total)
• Functional Keywords: protein synthesis, peptidyltransferase, ribozyme, ribonucleoprotein, ribosome
• Biological source: Deinococcus radiodurans; More
• Total number of polymer chains: 30
• Total formula weight: 1360337.59

Authors

Kaminishi, T.,Schedlbauer, A.,Ochoa-Lizarralde, B.,Connell, S.R.,Fucini, P. (deposition date: 2015-09-08, release date: 2015-11-11, Last modification date: 2016-02-03)

Primary citation

Kaminishi, T.,Schedlbauer, A.,Fabbretti, A.,Brandi, L.,Ochoa-Lizarralde, B.,He, C.G.,Milon, P.,Connell, S.R.,Gualerzi, C.O.,Fucini, P.
Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
Nucleic Acids Res., 43:10015-10025, 2015

PubMed Abstract: Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC.

PubMed: 26464437
DOI: 10.1093/nar/gkv975

Experimental method

X-RAY DIFFRACTION (2.9 Å)