3pd5 | pdb_00003pd5

Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with an analog of threonyl-adenylate

spinqualitylabelsall models 3pd5, resolution 2.29Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3pd5 is a 2 chain structure with sequence from "pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GOL, TSB Related: 2hl2, 2hl0, 2hl1, 1y2q, 3pd2, 3pd3, 3pd4 Gene: PAB1490, PYRAB13430, thrS ("Pyrococcus abyssi" Erauso et al. 1993) Activity: Threonine--tRNA ligase, with EC number 6.1.1.3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Editing/proofreading by aminoacyl-tRNA synthetases is an important quality control step in the accurate translation of the genetic code that removes noncognate amino acids attached to tRNA. Defects in the process of editing result in disease conditions including neurodegeneration. While proofreading, the cognate amino acids larger by a methyl group are generally thought to be sterically rejected by the editing modules as envisaged by the "Double-Sieve Model." Strikingly using solution based direct binding studies, NMR-heteronuclear single quantum coherence (HSQC) and isothermal titration calorimetry experiments, with an editing domain of threonyl-tRNA synthetase, we show that the cognate substrate can gain access and bind to the editing pocket. High-resolution crystal structural analyses reveal that functional positioning of substrates rather than steric exclusion is the key for the mechanism of discrimination. A strategically positioned "catalytic water" molecule is excluded to avoid hydrolysis of the cognate substrate using a "RNA mediated substrate-assisted catalysis mechanism" at the editing site. The mechanistic proof of the critical role of RNA in proofreading activity is a completely unique solution to the problem of cognate-noncognate selection mechanism. Mechanistic insights into cognate substrate discrimination during proofreading in translation.,Hussain T, Kamarthapu V, Kruparani SP, Deshmukh MV, Sankaranarayanan R Proc Natl Acad Sci U S A. 2010 Nov 22. PMID:21098258 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Aminoacyl tRNA Synthetase

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