1msy
From Proteopedia
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GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA
Overview
GNRA tetraloops (N is A, C, G, or U; R is A or G) are basic building, blocks of RNA structure that often interact with proteins or other RNA, structural elements. Understanding sequence-dependent structural variation, among different GNRA tetraloops is an important step toward elucidating, the molecular basis of specific GNRA tetraloop recognition by proteins and, RNAs. Details of the geometry and hydration of this motif have been based, on high-resolution crystallographic structures of the GRRA subset of, tetraloops; less is known about the GYRA subset (Y is C or U). We report, here the structure of a GUAA tetraloop determined to 1.4 A resolution to, better define these details and any distinctive features of GYRA, tetraloops. The tetraloop is part of a 27-nt structure that mimics the, universal sarcin/ricin loop from Escherichia coli 23S ribosomal RNA in, which a GUAA tetraloop replaces the conserved GAGA tetraloop. The, adenosines of the GUAA tetraloop form an intermolecular contact that is a, commonplace RNA tertiary interaction called an A-minor motif. This is the, first structure to reveal in great detail the geometry and hydration of a, GUAA tetraloop and an A-minor motif. Comparison of tetraloop structures, shows a common backbone geometry for each of the eight possible tetraloop, sequences and suggests a common hydration. After backbone atom, superposition, equivalent bases from different tetraloops unexpectedly, depart from coplanarity by as much as 48 degrees. This variation displaces, the functional groups of tetraloops implicated in protein and RNA binding, providing a recognition feature.
About this Structure
1MSY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution., Correll CC, Swinger K, RNA. 2003 Mar;9(3):355-63. PMID:12592009
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