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| | <StructureSection load='5b6j' size='340' side='right'caption='[[5b6j]], [[Resolution|resolution]] 2.43Å' scene=''> | | <StructureSection load='5b6j' size='340' side='right'caption='[[5b6j]], [[Resolution|resolution]] 2.43Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5b6j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibc3 Vibc3]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4y2z 4y2z]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B6J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5b6j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O395 Vibrio cholerae O395]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4y2z 4y2z]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B6J FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pth, VC0395_A1761, VC395_2298 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=345073 VIBC3])</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=5b6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b6j OCA], [https://pdbe.org/5b6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b6j RCSB], [https://www.ebi.ac.uk/pdbsum/5b6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b6j ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminoacyl-tRNA_hydrolase Aminoacyl-tRNA hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.29 3.1.1.29] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b6j OCA], [http://pdbe.org/5b6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b6j RCSB], [http://www.ebi.ac.uk/pdbsum/5b6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b6j ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PTH_VIBC3 PTH_VIBC3]] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. | + | [https://www.uniprot.org/uniprot/PTH_VIBC3 PTH_VIBC3] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aminoacyl-tRNA hydrolase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Vibc3]] | + | [[Category: Vibrio cholerae O395]] |
| - | [[Category: Arora, A]] | + | [[Category: Arora A]] |
| - | [[Category: Kabra, A]] | + | [[Category: Kabra A]] |
| - | [[Category: Pal, R K]] | + | [[Category: Pal RK]] |
| - | [[Category: Shahid, S]] | + | [[Category: Shahid S]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Mutant h24n]]
| + | |
| - | [[Category: Peptidyl-trna hydrolase]]
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| Structural highlights
Function
PTH_VIBC3 The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.
Publication Abstract from PubMed
Bacterial peptidyl-tRNA hydrolase (Pth; EC 3.1.1.29) hydrolyzes the peptidyl-tRNAs accumulated in the cytoplasm and thereby prevents cell death by alleviating tRNA starvation. X-ray and NMR studies of Vibrio cholerae Pth (VcPth) and mutants of its key residues involved in catalysis show that the activity and selectivity of the protein depends on the stereochemistry and dynamics of residues H24, D97, N118, and N14. D97-H24 interaction is critical for activity because it increases the nucleophilicity of H24. The N118 and N14 have orthogonally competing interactions with H24, both of which reduce the nucleophilicity of H24 and are likely to be offset by positioning of a peptidyl-tRNA substrate. The region proximal to H24 and the lid region exhibit slow motions that may assist in accommodating the substrate. Helix alpha3 exhibits a slow wobble with intermediate time scale motions of its N-cap residue N118, which may work as a flypaper to position the scissile ester bond of the substrate. Overall, the dynamics of interactions between the side chains of N14, H24, D97, and N118, control the catalysis of substrate by this enzyme.
Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase.,Kabra A, Shahid S, Pal RK, Yadav R, Pulavarti SV, Jain A, Tripathi S, Arora A RNA. 2017 Feb;23(2):202-216. doi: 10.1261/rna.057620.116. Epub 2016 Nov 10. PMID:28096445[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kabra A, Shahid S, Pal RK, Yadav R, Pulavarti SV, Jain A, Tripathi S, Arora A. Unraveling the stereochemical and dynamic aspects of the catalytic site of bacterial peptidyl-tRNA hydrolase. RNA. 2017 Feb;23(2):202-216. doi: 10.1261/rna.057620.116. Epub 2016 Nov 10. PMID:28096445 doi:http://dx.doi.org/10.1261/rna.057620.116
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