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| | ==2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol== | | ==2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol== |
| - | <StructureSection load='2dxi' size='340' side='right' caption='[[2dxi]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='2dxi' size='340' side='right'caption='[[2dxi]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dxi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DXI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dxi]] is a 4 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=2DXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DXI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GAU:(4S)-4-AMINO-5-HYDROXYPENTANOIC+ACID'>GAU</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gln|1gln]], [[1g59|1g59]], [[1j09|1j09]], [[1n75|1n75]], [[1n77|1n77]], [[1n78|1n78]], [[2cuz|2cuz]], [[2cv0|2cv0]], [[2cv1|2cv1]], [[2cv2|2cv2]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GAU:(4S)-4-AMINO-5-HYDROXYPENTANOIC+ACID'>GAU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] </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=2dxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxi OCA], [https://pdbe.org/2dxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dxi RCSB], [https://www.ebi.ac.uk/pdbsum/2dxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxi ProSAT], [https://www.topsan.org/Proteins/RSGI/2dxi TOPSAN]</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=2dxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dxi OCA], [http://pdbe.org/2dxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dxi RCSB], [http://www.ebi.ac.uk/pdbsum/2dxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dxi ProSAT], [http://www.topsan.org/Proteins/RSGI/2dxi TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8]] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</ref> | + | [https://www.uniprot.org/uniprot/SYE_THET8 SYE_THET8] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).<ref>PMID:11224561</ref> <ref>PMID:17161369</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]] | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| - | *[[TRNA|TRNA]] | + | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | + | [[Category: Large Structures]] |
| - | [[Category: Glutamate--tRNA ligase]] | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Sekine S]] |
| - | [[Category: Sekine, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama, S]] | + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Ligase-rna complex]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| Structural highlights
Function
SYE_THET8 Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).[1] [2]
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
Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly complementary L-glutamate-binding site. This collaborative site is functional, as it is formed in the same manner in pretransition-state mimic, GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic, GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is defective and accounts for the binding of incorrect amino acids, such as D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of the completely functional binding site for L-glutamate. These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation.
Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase.,Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S Structure. 2006 Dec;14(12):1791-9. PMID:17161369[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sekine S, Nureki O, Shimada A, Vassylyev DG, Yokoyama S. Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nat Struct Biol. 2001 Mar;8(3):203-6. PMID:11224561 doi:10.1038/84927
- ↑ Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S. Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure. 2006 Dec;14(12):1791-9. PMID:17161369 doi:10.1016/j.str.2006.10.005
- ↑ Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S. Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure. 2006 Dec;14(12):1791-9. PMID:17161369 doi:10.1016/j.str.2006.10.005
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