|
|
| Line 3: |
Line 3: |
| | <StructureSection load='1b7y' size='340' side='right'caption='[[1b7y]], [[Resolution|resolution]] 2.50Å' scene=''> | | <StructureSection load='1b7y' size='340' side='right'caption='[[1b7y]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1b7y]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B7Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1B7Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1b7y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B7Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FYA:ADENOSINE-5-[PHENYLALANINOL-PHOSPHATE]'>FYA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.5Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylalanine--tRNA_ligase Phenylalanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.20 6.1.1.20] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FYA:ADENOSINE-5-[PHENYLALANINOL-PHOSPHATE]'>FYA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1b7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b7y OCA], [http://pdbe.org/1b7y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b7y RCSB], [http://www.ebi.ac.uk/pdbsum/1b7y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b7y ProSAT]</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=1b7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b7y OCA], [https://pdbe.org/1b7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b7y RCSB], [https://www.ebi.ac.uk/pdbsum/1b7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b7y ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SYFA_THETH SYFA_THETH] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 35: |
Line 37: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Phenylalanine--tRNA ligase]] | |
| | [[Category: Thermus thermophilus]] | | [[Category: Thermus thermophilus]] |
| - | [[Category: Lavrik, O]] | + | [[Category: Lavrik O]] |
| - | [[Category: Moor, N]] | + | [[Category: Moor N]] |
| - | [[Category: Reshetnikova, L]] | + | [[Category: Reshetnikova L]] |
| - | [[Category: Vassylyev, D G]] | + | [[Category: Vassylyev DG]] |
| - | [[Category: Alpha/beta homodimer]]
| + | |
| - | [[Category: Enzyme]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Trna synthetase]]
| + | |
| Structural highlights
Function
SYFA_THETH
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
The crystal structures of Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) complexed with phenylalanine and phenylalaninyl-adenylate (PheOH-AMP), the synthetic analogue of phenylalanyl-adenylate, have been determined at 2.7A and 2.5A resolution, respectively. Both Phe and PheOH-AMP are engulfed in the active site cleft of the catalytic alpha-subunit of PheRS, and neither makes contact with the PheRS beta-subunit. The conformations and binding of Phe are almost identical in both complexes. The recognition of Phe by PheRS is achieved through a mixture of multiple van der Waals interactions and hydrogen bonds. The side-chain of the Phe substrate is sandwiched between the hydrophobic side-chains of Phealpha258 and Phealpha260 on one side, and the main-chain atoms of the two adjacent beta-strands on the other. The side-chains of Valalpha261 and Alaalpha314 form the back wall of the amino acid binding pocket. In addition, PheRS residues (Trpalpha149, Seralpha180, Hisalpha178, Argalpha204, Glnalpha218, and Glualpha220) form a total of seven hydrogen bonds with the main-chain atoms of Phe. The conformation of PheOH-AMP and the network of interactions of its AMP moiety with PheRS are reminiscent of the other class II synthetases. The structural similarity between PheRS and histidyl-tRNA synthetase extends to the amino acid binding site, which is normally unique for each enzyme. The complex structures suggest that the PheRS beta-subunit may affect the first step of the reaction (formation of phenylalanyl-adenylate) through the metal-mediated conserved alpha/beta-subunit interface. The modeling of tyrosine in the active site of PheRS revealed no apparent close contacts between tyrosine and the PheRS residues. This result implies that the proofreading mechanism against activated tyrosine, rather than direct recognition, may play the major role in the PheRS specificity.
Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.,Reshetnikova L, Moor N, Lavrik O, Vassylyev DG J Mol Biol. 1999 Apr 2;287(3):555-68. PMID:10092459[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Reshetnikova L, Moor N, Lavrik O, Vassylyev DG. Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue. J Mol Biol. 1999 Apr 2;287(3):555-68. PMID:10092459 doi:10.1006/jmbi.1999.2617
|
