2zm5

Crystal structure of tRNA modification enzyme MiaA in the complex with tRNA(Phe)

spinqualitylabelsall models 2zm5, resolution 2.55Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2zm5 is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MG NonStd Res: MSE Gene: miaA (Escherichia coli) Activity: tRNA dimethylallyltransferase, with EC number 2.5.1.75 Resources: FirstGlance, OCA, RCSB, PDBsum Function [MIAA_ECOLI] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed Bacterial and eukaryotic tRNAs that decode codons starting with uridine have a hydrophobically hypermodified adenosine at position 37 (A(37)) adjacent to the 3'-end of the anticodon, which is essential for efficient and highly accurate protein translation by the ribosome. However, it remains unclear as to how the corresponding tRNAs are selected to be modified by alkylation at the correct position of the adenosine base. We have determined a series of crystal structures of bacterial tRNA isopentenyltransferase (MiaA) in apo- and tRNA-bound forms, which completely render snapshots of substrate selections during the modification of RNA. A compact evolutionary inserted domain (herein swinging domain) in MiaA that exhibits as a highly mobile entity moves around the catalytic domain as likely to reach and trap the tRNA substrate. Thereby, MiaA clamps the anticodon stem loop of the tRNA substrate between the catalytic and swinging domains, where the two conserved elongated residues from the swinging domain pinch the two flanking A(36) and A(38) together to squeeze out A(37) into the reaction tunnel. The site-specific isopentenylation of RNA is thus ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection. Furthermore, combining information from soaking experiments with structural comparisons, we propose a mechanism for the ordered substrate binding of MiaA. Snapshots of Dynamics in Synthesizing N(6)-Isopentenyladenosine at the tRNA Anticodon.,Chimnaronk S, Forouhar F, Sakai J, Yao M, Tron CM, Atta M, Fontecave M, Hunt JF, Tanaka I Biochemistry. 2009 May 20. PMID:19435325 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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