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| | ==Crystal structure of peptidyl t-RNA hydrolase from Pseudomonas aeruginosa at 2.2 Angstrom resolution== | | ==Crystal structure of peptidyl t-RNA hydrolase from Pseudomonas aeruginosa at 2.2 Angstrom resolution== |
| - | <StructureSection load='4fno' size='340' side='right' caption='[[4fno]], [[Resolution|resolution]] 2.25Å' scene=''> | + | <StructureSection load='4fno' size='340' side='right'caption='[[4fno]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fno]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FNO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FNO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fno]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FNO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FNO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4erx|4erx]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pth ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4fno FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fno OCA], [https://pdbe.org/4fno PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fno RCSB], [https://www.ebi.ac.uk/pdbsum/4fno PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fno 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>
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| - | <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=4fno FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fno OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fno RCSB], [http://www.ebi.ac.uk/pdbsum/4fno PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PTH_PSEAE PTH_PSEAE]] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (By similarity). | + | [https://www.uniprot.org/uniprot/PTH_PSEAE PTH_PSEAE] 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4fno" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aminoacyl-tRNA hydrolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Pseae]] | + | [[Category: Pseudomonas aeruginosa PAO1]] |
| - | [[Category: Arora, A]] | + | [[Category: Arora A]] |
| - | [[Category: Kaur, P]] | + | [[Category: Kaur P]] |
| - | [[Category: Kumar, A]] | + | [[Category: Kumar A]] |
| - | [[Category: Sharma, S]] | + | [[Category: Sharma S]] |
| - | [[Category: Singh, A]] | + | [[Category: Singh A]] |
| - | [[Category: Singh, N]] | + | [[Category: Singh N]] |
| - | [[Category: Singh, T P]] | + | [[Category: Singh TP]] |
| - | [[Category: Sinha, M]] | + | [[Category: Sinha M]] |
| - | [[Category: Hydrolase]]
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| Structural highlights
Function
PTH_PSEAE The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (By similarity).
Publication Abstract from PubMed
During the course of protein synthesis in the cell, the translation process is often terminated due to various reasons. As a result, peptidyl-tRNA molecules are released which are toxic to the cell as well reducing the availability of free amino acid and tRNA molecules for the required protein synthesis in the cell. Such a situation is corrected by an enzyme, Pth (peptidyl-tRNA hydrolase), which catalyses the release of free tRNA and peptide moieties from peptidyl-tRNAs. This means that the active Pth is essential for the survival of bacteria. In order to design inhibitors of PaPth (Pth from Pseudomonas aeruginosa), we determined the structures of PaPth in its native and bound states with compounds amino acylate-tRNA analogue and 5-azacytidine. The structure determination of the native protein revealed that the substrate-binding site was partially occupied by Glu161 from the neigh-bouring molecule. The structure of PaPth indicated that the substrate-binding site can be broadly divided into three distinct subsites. The structures of the two complexes showed that the amino acylate-tRNA analogue filled three subsites, whereas 5-azacytidine filled two subsites. The common sugar and the base moieties of the two compounds occupied identical positions in the cleft. Using surface plasmon resonance, the dissociation constants for the amino acylate-tRNA analogue and 5-azacytidine were found to be 3.53x10-8 M and 5.82x10-8 M respectively.
Structural and binding studies of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa provide a platform for the structure-based inhibitor design against peptidyl-tRNA hydrolase.,Singh A, Kumar A, Gautam L, Sharma P, Sinha M, Bhushan A, Kaur P, Sharma S, Arora A, Singh TP Biochem J. 2014 Nov 1;463(3):329-37. doi: 10.1042/BJ20140631. PMID:25101795[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Singh A, Kumar A, Gautam L, Sharma P, Sinha M, Bhushan A, Kaur P, Sharma S, Arora A, Singh TP. Structural and binding studies of peptidyl-tRNA hydrolase from Pseudomonas aeruginosa provide a platform for the structure-based inhibitor design against peptidyl-tRNA hydrolase. Biochem J. 2014 Nov 1;463(3):329-37. doi: 10.1042/BJ20140631. PMID:25101795 doi:http://dx.doi.org/10.1042/BJ20140631
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