2naf: Difference between revisions
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The | ==Solution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis== | ||
<StructureSection load='2naf' size='340' side='right'caption='[[2naf]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2naf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NAF FirstGlance]. <br> | |||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2naf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2naf OCA], [https://pdbe.org/2naf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2naf RCSB], [https://www.ebi.ac.uk/pdbsum/2naf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2naf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PTH_MYCS2 PTH_MYCS2] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (By similarity). | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:27378575</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 2naf" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Peptidyl-tRNA hydrolase|Peptidyl-tRNA hydrolase]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: Pathak | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Mycolicibacterium smegmatis MC2 155]] | |||
[[Category: Arora A]] | |||
[[Category: Fatma F]] | |||
[[Category: Jain A]] | |||
[[Category: Kabra A]] | |||
[[Category: Kumar A]] | |||
[[Category: Pathak P]] | |||
[[Category: Pulavarti S]] | |||
[[Category: Shukla V]] | |||
[[Category: Yadav R]] | |||
Latest revision as of 13:25, 15 March 2023
Solution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatisSolution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis
Structural highlights
FunctionPTH_MYCS2 The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (By similarity). Publication Abstract from PubMedBACKGROUND: 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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