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. 2011 Jul 6;9:47. doi: 10.1186/1741-7007-9-47

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Copyright ©2011 Korennykh et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Model of stem-loop recognition via a composite protein surface. (a) Stem-loops derived from XBP1 mRNA (HP21) and phenylalanine tRNA^Phe(tPhe). Loop sequence differences are colored yellow in tPhe. (b) Time courses (0-5 min) for cleavage of 5'-³²P-labeled stem-loops HP21 and tPhe by Ire1KR32 (3 μM) analyzed by polyacrylamide gel electrophoresis. (c) Superposition of crystal structures of tRNA^Phe(PDB ID 1ehz) and tRNA^Phefrom tRNA^Phe·MiaA complex (PDB ID 2zm5). Black arrow shows direction of nucleophile attack, orange arrow shows direction of leaving group. (d) Manual rigid-body docking of the base-flipped tRNA^Pheanticodon into Ire1 crystal structure. Electron density for the scissile phosphate (contoured at 12σ) and the proposed catalytic mechanism (Figure 3c-I) were used as docking constraints. P designates scissile phosphate. The helix-loop element (HLE) is colored green. (e) Surface rendering of the model in (d). The model suggests cleavage of a stem-loop by one active site and recognition by a composite RNA binding surface.