2ogn
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The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080
OverviewOverview
New insights into functional flexibility at the peptidyl transferase, center (PTC) and its vicinity were obtained by analysis of pleuromutilins, binding modes to the ribosome. The crystal structures of Deinococcus, radiodurans large ribosomal subunit complexed with each of three, pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and, SB-571519, show that all bind to the PTC with their core oriented, similarly at the A-site and their C14 extensions pointing toward the, P-site. Except for an H-bond network with a single nucleotide, G2061, which involves the essential keto group of all three compounds, only minor, hydrophobic contacts are formed between the pleuromutilin C14 extensions, and any ribosomal component, consistent with the PTC tolerance to amino, acid diversity. Efficient drug binding mode is attained by a mechanism, based on induced-fit motions exploiting the ribosomal intrinsic functional, flexibility and resulting in conformational rearrangements that seal the, pleuromutilin-binding pocket and tightens it up. Comparative studies, identified a network of remote interactions around the PTC, indicating, that pleuromutilins selectivity is acquired by nonconserved nucleotides, residing in the PTC vicinity, in a fashion resembling allosterism., Likewise, pleuromutilin resistant mechanisms involve nucleotides residing, in the environs of the binding pocket, consistent with their slow, resistance-development rates.
About this StructureAbout this Structure
2OGN is a Single protein structure of sequence from Deinococcus radiodurans with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity., Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A, Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4291-6. Epub 2007 Mar 8. PMID:17360517
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