3a05: Difference between revisions

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<StructureSection load='3a05' size='340' side='right'caption='[[3a05]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3a05' size='340' side='right'caption='[[3a05]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3a05]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A05 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3a05]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A05 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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]] 2.2&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a04|3a04]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trpS, APE_2461.1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 AERPX])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </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=3a05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a05 OCA], [https://pdbe.org/3a05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a05 RCSB], [https://www.ebi.ac.uk/pdbsum/3a05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a05 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=3a05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a05 OCA], [https://pdbe.org/3a05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a05 RCSB], [https://www.ebi.ac.uk/pdbsum/3a05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a05 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYW_AERPE SYW_AERPE]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=3a05 ConSurf].
</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=3a05 ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The identity elements of transfer RNA are the molecular basis for recognition by each cognate aminoacyl-tRNA synthetase. In the archaea system, the tryptophan tRNA identity has not been determined in detail. To investigate the molecular recognition mechanism of tryptophan tRNA by tryptophanyl-tRNA synthetase (TrpRS) from the hyperthermophilic and aerobic archaeon, Aeropyrum pernix K1, various mutant transcripts of tryptophan tRNA prepared by an in vitro transcription system were examined by overexpression of A. pernix TrpRS. Substitution of the discriminator base, A73, impaired tryptophan incorporation activity. Changing the G1-C72 base pair to other base pairs also decreased the aminoacylation activity. Substitutions of anticodon CCA revealed that the C34 and C35 mutants dramatically reduced aminoacylation with tryptophan, but the A36 mutants had the same activity as the wild type. The results indicate that the anticodon nucleotides C34, C35, discriminator base A73 and G1-C72 base pair are major recognition sites for A. pernix TrpRS.
Molecular recognition of tryptophan tRNA by tryptophanyl-tRNA synthetase from Aeropyrum pernix K1.,Tsuchiya W, Hasegawa T J Biochem. 2009 May;145(5):635-41. Epub 2009 Jan 29. PMID:19179361<ref>PMID:19179361</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3a05" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Aerpx]]
[[Category: Aeropyrum pernix]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Tryptophan--tRNA ligase]]
[[Category: Fujimoto Z]]
[[Category: Fujimoto, Z]]
[[Category: Hasegawa T]]
[[Category: Hasegawa, T]]
[[Category: Tsuchiya W]]
[[Category: Tsuchiya, W]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Atp-binding]]
[[Category: Cytoplasm]]
[[Category: Ligase]]
[[Category: Nucleotide-binding]]
[[Category: Protein biosynthesis]]
[[Category: Tryptophanyl-trna synthetase]]

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