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| | ==Crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus== | | ==Crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus== |
| - | <StructureSection load='5zx8' size='340' side='right' caption='[[5zx8]], [[Resolution|resolution]] 1.00Å' scene=''> | + | <StructureSection load='5zx8' size='340' side='right'caption='[[5zx8]], [[Resolution|resolution]] 1.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zx8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZX8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZX8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zx8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZX8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZX8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pth, TTHA1588 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5zx8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zx8 OCA], [https://pdbe.org/5zx8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zx8 RCSB], [https://www.ebi.ac.uk/pdbsum/5zx8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zx8 ProSAT]</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=5zx8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zx8 OCA], [http://pdbe.org/5zx8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zx8 RCSB], [http://www.ebi.ac.uk/pdbsum/5zx8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zx8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PTH_THET8 PTH_THET8]] The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis. | + | [https://www.uniprot.org/uniprot/PTH_THET8 PTH_THET8] 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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| | </div> | | </div> |
| | <div class="pdbe-citations 5zx8" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5zx8" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Peptidyl-tRNA hydrolase|Peptidyl-tRNA hydrolase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aminoacyl-tRNA hydrolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Thet8]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Ito, K]] | + | [[Category: Ito K]] |
| - | [[Category: Matsumoto, A]] | + | [[Category: Matsumoto A]] |
| - | [[Category: Shimizu, Y]] | + | [[Category: Shimizu Y]] |
| - | [[Category: Uchiumi, T]] | + | [[Category: Uchiumi T]] |
| - | [[Category: Ueda, T]] | + | [[Category: Ueda T]] |
| - | [[Category: Uehara, U]] | + | [[Category: Uehara U]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Peptidyl-trna hydrolase]]
| + | |
| - | [[Category: Thermus thermophilus]]
| + | |
| Structural highlights
Function
PTH_THET8 The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis.
Publication Abstract from PubMed
Peptidyl-tRNA hydrolase (Pth) cleaves the ester bond between the peptide and the tRNA of peptidyl-tRNA molecules, which are the products of defective translation, to recycle the tRNA for further rounds of protein synthesis. Pth is ubiquitous in nature, and its activity is essential for bacterial viability. Here, we have determined the crystal structure of Pth from Thermus thermophilus (TtPth) at 1.00 A resolution. This is the first structure of a Pth from a thermophilic bacterium and the highest resolution Pth structure reported so far. The present atomic resolution data enabled the calculation of anisotropic displacement parameters for all atoms, which revealed the directionality of the fluctuations of key regions for the substrate recognition. Comparisons between TtPth and mesophilic bacterial Pths revealed that their structures are similar overall. However, the structures of the N- and C-terminal, loop-helix alpha4, and helix alpha6 regions are different. In addition, the helix alpha1 to strand beta4 region of TtPth is remarkably different from those of the mesophilic bacterial Pths, because this region is 9 or 10 amino acid residues shorter than those of the mesophilic bacterial Pths. This shortening seems to contribute to the thermostability of TtPth. To further understand the determinants for the thermostability of TtPth, we compared various structural factors of TtPth with those of mesophilic bacterial Pths. The data suggest that the decreases in accessible surface area and thermolabile amino acid residues, and the increases in ion pairs, hydrogen bonds, and proline residues cooperatively contribute to the thermostability of TtPth.
High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus.,Matsumoto A, Uehara Y, Shimizu Y, Ueda T, Uchiumi T, Ito K Proteins. 2019 Mar;87(3):226-235. doi: 10.1002/prot.25643. Epub 2018 Dec 27. PMID:30520515[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Matsumoto A, Uehara Y, Shimizu Y, Ueda T, Uchiumi T, Ito K. High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus. Proteins. 2019 Mar;87(3):226-235. doi: 10.1002/prot.25643. Epub 2018 Dec 27. PMID:30520515 doi:http://dx.doi.org/10.1002/prot.25643
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