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| | ==Methionyl-tRNA synthetase from Escherichia coli complexed with methionine phosphonate== | | ==Methionyl-tRNA synthetase from Escherichia coli complexed with methionine phosphonate== |
| - | <StructureSection load='1p7p' size='340' side='right' caption='[[1p7p]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='1p7p' size='340' side='right'caption='[[1p7p]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1p7p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P7P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1p7p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P7P FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPH:(1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHONIC+ACID'>MPH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pfu|1pfu]], [[1pfv|1pfv]], [[1pfw|1pfw]], [[1pfy|1pfy]], [[1pg0|1pg0]], [[1pg2|1pg2]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPH:(1-AMINO-3-METHYLSULFANYL-PROPYL)-PHOSPHONIC+ACID'>MPH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">METG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7p OCA], [https://pdbe.org/1p7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p7p RCSB], [https://www.ebi.ac.uk/pdbsum/1p7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7p 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/Methionine--tRNA_ligase Methionine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.10 6.1.1.10] </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=1p7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p7p OCA], [http://pdbe.org/1p7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p7p RCSB], [http://www.ebi.ac.uk/pdbsum/1p7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p7p ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SYM_ECOLI SYM_ECOLI]] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.[HAMAP-Rule:MF_00098] | + | [https://www.uniprot.org/uniprot/SYM_ECOLI SYM_ECOLI] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.[HAMAP-Rule:MF_00098] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1p7p" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1p7p" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Methionine--tRNA ligase]] | + | [[Category: Large Structures]] |
| - | [[Category: Blanquet, S]] | + | [[Category: Blanquet S]] |
| - | [[Category: Crepin, T]] | + | [[Category: Crepin T]] |
| - | [[Category: Honek, J F]] | + | [[Category: Honek JF]] |
| - | [[Category: Mechulam, Y]] | + | [[Category: Mechulam Y]] |
| - | [[Category: Sampson, P B]] | + | [[Category: Sampson PB]] |
| - | [[Category: Schmitt, E]] | + | [[Category: Schmitt E]] |
| - | [[Category: Vaughan, M D]] | + | [[Category: Vaughan MD]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
SYM_ECOLI Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.[HAMAP-Rule:MF_00098]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Binding of methionine to methionyl-tRNA synthetase (MetRS) is known to promote conformational changes within the active site. However, the contribution of these rearrangements to enzyme catalysis is not fully understood. In this study, several methionine and methionyl adenylate analogues were diffused into crystals of the monomeric form of Escherichia coli methionyl-tRNA synthetase. The structures of the corresponding complexes were solved at resolutions below 1.9A and compared to those of the enzyme free or complexed with methionine. Residues Y15 and W253 play key roles in the strength of the binding of the amino acid and of its analogues. Indeed, full motions of these residues are required to recover the maximum in free energy of binding. Residue Y15 also controls the size of the hydrophobic pocket where the amino acid side-chain interacts. H301 appears to participate to the specific recognition of the sulphur atom of methionine. Complexes with methionyl adenylate analogues illustrate the shielding by MetRS of the region joining the methionine and adenosine moieties. Finally, the structure of MetRS complexed to a methionine analogue mimicking the tetrahedral carbon of the transition state in the aminoacylation reaction was solved. On the basis of this model, we propose that, in response to the binding of the 3'-end of tRNA, Y15 moves again in order to deshield the anhydride bond in the natural adenylate.
Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase.,Crepin T, Schmitt E, Mechulam Y, Sampson PB, Vaughan MD, Honek JF, Blanquet S J Mol Biol. 2003 Sep 5;332(1):59-72. PMID:12946347[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Crepin T, Schmitt E, Mechulam Y, Sampson PB, Vaughan MD, Honek JF, Blanquet S. Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase. J Mol Biol. 2003 Sep 5;332(1):59-72. PMID:12946347
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