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1wyd

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[[Image:1wyd.gif|left|200px]]<br /><applet load="1wyd" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wyd, resolution 2.30&Aring;" />
 
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'''Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii'''<br />
 
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==Overview==
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==Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii==
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In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNA(Asn) in addition to Asp-tRNA(Asp). In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St-AspRS (nondiscriminating type) has been determined at 2.3 A resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer.
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<StructureSection load='1wyd' size='340' side='right'caption='[[1wyd]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1wyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WYD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyd OCA], [https://pdbe.org/1wyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wyd RCSB], [https://www.ebi.ac.uk/pdbsum/1wyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYDND_SULTO SYDND_SULTO] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps: L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).[HAMAP-Rule:MF_02075]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1wyd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1WYD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_tokodaii Sulfolobus tokodaii] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=EPE:'>EPE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WYD OCA].
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons., Sato Y, Maeda Y, Shimizu S, Hossain MT, Ubukata S, Suzuki K, Sekiguchi T, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1042-7. Epub 2007, Sep 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17881821 17881821]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Sulfurisphaera tokodaii str. 7]]
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[[Category: Sulfolobus tokodaii]]
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[[Category: Hossain MT]]
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[[Category: Hossain, M T.]]
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[[Category: Maeda Y]]
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[[Category: Maeda, Y.]]
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[[Category: Sekiguchi T]]
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[[Category: Sekiguchi, T.]]
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[[Category: Suzuki K]]
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[[Category: Suzuki, K.]]
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[[Category: Takenaka A]]
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[[Category: Takenaka, A.]]
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[[Category: Ubukata S]]
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[[Category: Ubukata, S.]]
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[[Category: CL]]
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[[Category: EPE]]
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[[Category: SO4]]
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[[Category: archaea]]
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[[Category: aspartyl-trna synthetase]]
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[[Category: ligase]]
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[[Category: sulfolobus tokodaii]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:49:19 2008''
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Current revision

Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii

PDB ID 1wyd

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