1N8R

Structure of large ribosomal subunit in complex with virginiamycin M

Summary for 1N8R

• Entry DOI: 10.2210/pdb1n8r/pdb
• Related: 1FFK 1JJ2 1K73 1KC8
• Descriptor: 23S ribosomal RNA, 50S ribosomal protein L10e, 50S ribosomal protein L13P, ... (37 entities in total)
• Functional Keywords: ribosome-antibiotic complex, virginiamycin m, streptogramin, antibiotic, ribosome/antibiotic
• Biological source: Haloarcula marismortui; More
• Total number of polymer chains: 30
• Total formula weight: 1458641.69

Authors

Hansen, J.L.,Moore, P.B.,Steitz, T.A. (deposition date: 2002-11-21, release date: 2003-07-22, Last modification date: 2024-03-13)

Primary citation

Hansen, J.,Moore, P.B.,Steitz, T.A.
Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit
J.Mol.Biol., 330:1061-1075, 2003

PubMed Abstract: Structures of anisomycin, chloramphenicol, sparsomycin, blasticidin S, and virginiamycin M bound to the large ribosomal subunit of Haloarcula marismortui have been determined at 3.0A resolution. Most of these antibiotics bind to sites that overlap those of either peptidyl-tRNA or aminoacyl-tRNA, consistent with their functioning as competitive inhibitors of peptide bond formation. Two hydrophobic crevices, one at the peptidyl transferase center and the other at the entrance to the peptide exit tunnel play roles in binding these antibiotics. Midway between these crevices, nucleotide A2103 of H.marismortui (2062 Escherichia coli) varies in its conformation and thereby contacts antibiotics bound at either crevice. The aromatic ring of anisomycin binds to the active-site hydrophobic crevice, as does the aromatic ring of puromycin, while the aromatic ring of chloramphenicol binds to the exit tunnel hydrophobic crevice. Sparsomycin contacts primarily a P-site bound substrate, but also extends into the active-site hydrophobic crevice. Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA.

PubMed: 12860128
DOI: 10.1016/S0022-2836(03)00668-5

Experimental method

X-RAY DIFFRACTION (3 Å)