2d6f: Difference between revisions

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New page: left|200px<br /><applet load="2d6f" size="450" color="white" frame="true" align="right" spinBox="true" caption="2d6f, resolution 3.15Å" /> '''Crystal structure of...
 
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[[Image:2d6f.gif|left|200px]]<br /><applet load="2d6f" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2d6f, resolution 3.15&Aring;" />
'''Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)'''<br />


==Overview==
==Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)==
Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a, pretranslational amidation of misacylated Glu-tRNA(Gln) by the, heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the, crystal structure of the Methanothermobacter thermautotrophicus GatDE, complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis, of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for, the enzyme's three reactions (glutaminase, kinase, and amidotransferase, activity). A 40 angstrom-long channel for ammonia transport connects the, active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout, based on shape complementarity of the D loop suggests an early, anticodon-independent RNA-based mechanism for adding glutamine to the, genetic code.
<StructureSection load='2d6f' size='340' side='right'caption='[[2d6f]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2d6f]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D6F 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]] 3.15&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2d6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d6f OCA], [https://pdbe.org/2d6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d6f RCSB], [https://www.ebi.ac.uk/pdbsum/2d6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d6f ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GATD_METTH GATD_METTH] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate.
== 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/d6/2d6f_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=2d6f ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2D6F is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2D6F OCA].
*[[Glutamyl-tRNA(Gln) amidotransferase|Glutamyl-tRNA(Gln) amidotransferase]]
 
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
==Reference==
__TOC__
Structural basis of RNA-dependent recruitment of glutamine to the genetic code., Oshikane H, Sheppard K, Fukai S, Nakamura Y, Ishitani R, Numata T, Sherrer RL, Feng L, Schmitt E, Panvert M, Blanquet S, Mechulam Y, Soll D, Nureki O, Science. 2006 Jun 30;312(5782):1950-4. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16809540 16809540]
</StructureSection>
[[Category: Large Structures]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Protein complex]]
[[Category: Nureki O]]
[[Category: Nureki, O.]]
[[Category: ZN]]
[[Category: ligase]]
[[Category: rna]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:28:03 2007''

Latest revision as of 16:46, 13 March 2024

Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)Crystal structure of Glu-tRNA(Gln) amidotransferase in the complex with tRNA(Gln)

Structural highlights

2d6f is a 6 chain structure with sequence from Methanothermobacter thermautotrophicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.15Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GATD_METTH Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The GatDE system is specific for glutamate and does not act on aspartate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2d6f, resolution 3.15Å

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