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[[Image:1n78.gif|left|200px]]
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{{STRUCTURE_1n78|  PDB=1n78  |  SCENE=  }}
'''Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.'''


==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.==
<StructureSection load='1n78' size='340' side='right'caption='[[1n78]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1n78]] 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=1N78 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N78 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOM:GLUTAMOL-AMP'>GOM</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'>[https://proteopedia.org/fgij/fg.htm?mol=1n78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n78 OCA], [https://pdbe.org/1n78 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n78 RCSB], [https://www.ebi.ac.uk/pdbsum/1n78 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n78 ProSAT], [https://www.topsan.org/Proteins/RSGI/1n78 TOPSAN]</span></td></tr>
</table>
== Function ==
[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 ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n78_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n78 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.


==Overview==
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.,Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S EMBO J. 2003 Feb 3;22(3):676-88. PMID:12554668<ref>PMID:12554668</ref>
Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1N78 is a [[Single protein]] structure of 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=1N78 OCA].
</div>
<div class="pdbe-citations 1n78" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding., Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S, EMBO J. 2003 Feb 3;22(3):676-88. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12554668 12554668]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
[[Category: Glutamate--tRNA ligase]]
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
[[Category: Single protein]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Bernier, S.]]
[[Category: Bernier S]]
[[Category: Chenevert, R.]]
[[Category: Chenevert R]]
[[Category: Dubois, D Y.]]
[[Category: Dubois DY]]
[[Category: Lapointe, J.]]
[[Category: Lapointe J]]
[[Category: Nureki, O.]]
[[Category: Nureki O]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Sekine S]]
[[Category: Sekine, S.]]
[[Category: Vassylyev DG]]
[[Category: Vassylyev, D G.]]
[[Category: Yokoyama S]]
[[Category: Yokoyama, S.]]
[[Category: Ers/trna/goa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:10:54 2008''

Latest revision as of 10:19, 25 October 2023

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.

Structural highlights

1n78 is a 4 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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

Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.

ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.,Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S EMBO J. 2003 Feb 3;22(3):676-88. PMID:12554668[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J. 2003 Feb 3;22(3):676-88. PMID:12554668 doi:http://dx.doi.org/10.1093/emboj/cdg053

1n78, resolution 2.10Å

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