3epk | pdb_00003epk

Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: Insight into tRNA recognition and reaction mechanism

spinqualitylabelsall models 3epk, resolution 3.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3epk is a 4 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: DST, MG, PPV, ZN Related: 3eph, 3epj, 3epl Gene: MOD5 (ATCC 18824) Activity: tRNA dimethylallyltransferase, with EC number 2.5.1.75 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [MOD5_YEAST] Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in the anticodon loop on a specific subset of tRNAs both in the cytosol and the mitochondrion, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A). This modification optimizes the codon:anticodon fit in the ribosome and promotes translational fidelity. Competes with the farnesyl pyrophosphate synthase ERG20 for the common substrate dimethylallyl diphosphate (DMAPP). 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 Hypermodifications near the anticodon of tRNA are fundamental for the efficiency and fidelity of protein synthesis. Dimethylallyltransferase (DMATase) catalyzes transfer of a dimethylallyl moiety from dimethylallyl pyrophosphate to N6 of A37 in certain tRNAs. Here we present the crystal structures of Saccharomyces cerevisiae DMATase-tRNA(Cys) complex in four distinct forms, which provide snapshots of the RNA modification reaction catalyzed by DMATase. The structures reveal that the enzyme recognizes the tRNA substrate through indirect sequence readout. The targeted nucleotide A37 flips out from the anticodon loop of tRNA and flips into a channel in DMATase, where it meets its reaction partner di methylallyl pyrophosphate, which enters the channel from the opposite end. Structural changes accompanying the transfer reaction taking place in the crystal result in disengagement of DMATase-tRNA interaction near the reaction center. In addition, structural comparison of DMATase in the complex with unliganded bacterial DMATase provides a molecular basis of ordered substrate binding by DMATase. Crystallographic snapshots of eukaryotic dimethylallyltransferase acting on tRNA: insight into tRNA recognition and reaction mechanism.,Zhou C, Huang RH Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7. Epub 2008 Oct 13. PMID:18852462 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Transfer RNA (tRNA)

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