2dxi: Difference between revisions

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{{Seed}}
[[Image:2dxi.png|left|200px]]


<!--
==2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol==
The line below this paragraph, containing "STRUCTURE_2dxi", creates the "Structure Box" on the page.
<StructureSection load='2dxi' size='340' side='right'caption='[[2dxi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<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>
{{STRUCTURE_2dxi|  PDB=2dxi  |  SCENE=  }}
<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>
</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/dx/2dxi_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=2dxi ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.


===2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol===
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<ref>PMID:17161369</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2dxi" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17161369}}, adds the Publication Abstract to the page
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17161369 is the PubMed ID number.
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-->
== References ==
{{ABSTRACT_PUBMED_17161369}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
2DXI is a 4 chains structure of sequences 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=2DXI OCA].
[[Category: Large Structures]]
 
==Reference==
<ref group="xtra">PMID:17161369</ref><references group="xtra"/>
[[Category: Glutamate--tRNA ligase]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Sekine S]]
[[Category: Sekine, S.]]
[[Category: Yokoyama S]]
[[Category: Yokoyama, S.]]
[[Category: Ligase]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rna]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:03:34 2009''

Latest revision as of 11:31, 25 October 2023

2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol

Structural highlights

2dxi 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 2.2Å
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

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

  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, 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

2dxi, resolution 2.20Å

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