2naf | pdb_00002naf

Solution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis

spinqualitylabelsall models 2naf, 10 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2naf is a 1 chain structure with sequence from Mycs2. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Gene: MSMEG_5432, MSMEI_5283, pth (MYCS2) Activity: Aminoacyl-tRNA hydrolase, with EC number 3.1.1.29 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [PTH_MYCS2] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (By similarity). Publication Abstract from PubMed BACKGROUND: Accumulation of toxic peptidyl-tRNAs in the bacterial cytoplasm is averted by the action of peptidyl-tRNA hydrolase (Pth), which cleaves peptidyl-tRNA into free tRNA and peptide. NMR studies are needed for a protein homolog with a complete crystal structure, for comparison with the NMR structure of Mycobacterium tuberculosis Pth. METHODS: The structure and dynamics of Mycobacterium smegmatis Pth (MsPth) were characterized by NMR spectroscopy and MD simulations. The thermal stability of MsPth was characterized by DSC. RESULTS: MsPth NMR structure has a central mixed seven stranded beta-sheet that is enclosed by six alpha-helices. NMR relaxation and MD simulations studies show that most of the ordered regions are rigid. Of the substrate binding segments, the gate loop is rigid, the base loop displays slow motions, while the lid loop displays fast timescale motions. MsPth displays high thermal stability characterized by a melting temperature of 61.71 degrees C. CONCLUSION: The NMR structure of MsPth shares the canonical Pth fold with the NMR structure of MtPth. The motional characteristics for the lid region, the tip of helix alpha3, and the gate region, as indicated by MD simulations and NMR data, are similar for MsPth and MtPth. However, MsPth has relatively less rigid base loop and more compactly packed helices alpha5 and alpha6. The packing and the dynamic differences appear to be an important contributing factor to the thermal stability of MsPth, which is significantly higher than that of MtPth. SIGNIFICANCE: MsPth structure consolidates our understanding of the structure and dynamics of bacterial Pth proteins. Structural characterization of peptidyl-tRNA hydrolase from Mycobacterium smegmatis by NMR spectroscopy.,Kabra A, Fatma F, Shahid S, Pathak PP, Yadav R, Pulavarti SV, Tripathi S, Jain A, Arora A Biochim Biophys Acta. 2016 Oct;1864(10):1304-14. doi:, 10.1016/j.bbapap.2016.06.013. Epub 2016 Jul 2. PMID:27378575 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Peptidyl-tRNA hydrolase

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