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1yfr

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(New page: 200px<br /><applet load="1yfr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yfr, resolution 2.15&Aring;" /> '''crystal structure of...)
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[[Image:1yfr.gif|left|200px]]<br /><applet load="1yfr" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yfr, resolution 2.15&Aring;" />
 
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'''crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium'''<br />
 
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==Overview==
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==crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium==
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The genetic code is fixed in aminoacylation reactions catalyzed by, aminoacyl-tRNA synthetases. Amino acid discrimination occurs at two sites:, one for amino acid activation and aminoacylation and one for editing, misactivated amino acids. Although the active site sieves out bulkier, amino acids, misactivation occurs with substrates whose side chains are, smaller than the cognate one. Paradoxically, although alanyl-tRNA, synthetase activates glycine as well as alanine, the sterically larger, (than alanine) serine is also misactivated. Here, we report crystal, structures of an active fragment of Aquifex aeolicus alanyl-tRNA, synthetase complexed, separately, with Mg2+-ATP, alanine, glycine, and, serine. Ala and Gly are bound in similar orientations in a, side-chain-accommodating pocket, where alpha-amino and carboxyl groups are, stabilized by salt bridges, and the carboxyl by an H-bond from the side, chain NH2 of Asn-194. In contrast, whereas the same two salt bridges, stabilize bound Ser, H-bonding of the highly conserved (among class II, tRNA synthetases) Asn-194 side chain NH2 to the Ser OH, instead of to the, carboxyl, forces pocket expansion. Significantly, in the Mg2+-ATP complex, Asn-194 coordinates a Mg2+-alpha-phosphate bridge. Thus, the sieve for Ser, exclusion is broken because of selective pressure to retain Asn-194 for, Mg2+-ATP and Ala binding.
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<StructureSection load='1yfr' size='340' side='right'caption='[[1yfr]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yfr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YFR 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]] 2.15&#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=MG:MAGNESIUM+ION'>MG</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=1yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yfr OCA], [https://pdbe.org/1yfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yfr RCSB], [https://www.ebi.ac.uk/pdbsum/1yfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yfr ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYA_AQUAE SYA_AQUAE] Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction: alanine is first activated by ATP to form Ala-AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain (By similarity).[HAMAP-Rule:MF_00036]
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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/yf/1yfr_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=1yfr ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-tRNA synthetases. Amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. Although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. Paradoxically, although alanyl-tRNA synthetase activates glycine as well as alanine, the sterically larger (than alanine) serine is also misactivated. Here, we report crystal structures of an active fragment of Aquifex aeolicus alanyl-tRNA synthetase complexed, separately, with Mg2+-ATP, alanine, glycine, and serine. Ala and Gly are bound in similar orientations in a side-chain-accommodating pocket, where alpha-amino and carboxyl groups are stabilized by salt bridges, and the carboxyl by an H-bond from the side chain NH2 of Asn-194. In contrast, whereas the same two salt bridges stabilize bound Ser, H-bonding of the highly conserved (among class II tRNA synthetases) Asn-194 side chain NH2 to the Ser OH, instead of to the carboxyl, forces pocket expansion. Significantly, in the Mg2+-ATP complex, Asn-194 coordinates a Mg2+-alpha-phosphate bridge. Thus, the sieve for Ser exclusion is broken because of selective pressure to retain Asn-194 for Mg2+-ATP and Ala binding.
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==About this Structure==
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Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase.,Swairjo MA, Schimmel PR Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):988-93. Epub 2005 Jan 18. PMID:15657145<ref>PMID:15657145</ref>
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1YFR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with MG and ATP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alanine--tRNA_ligase Alanine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.7 6.1.1.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YFR OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase., Swairjo MA, Schimmel PR, Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):988-93. Epub 2005 Jan 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15657145 15657145]
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</div>
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[[Category: Alanine--tRNA ligase]]
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<div class="pdbe-citations 1yfr" style="background-color:#fffaf0;"></div>
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[[Category: Aquifex aeolicus]]
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[[Category: Single protein]]
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[[Category: Schimmel, P.R.]]
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[[Category: Swairjo, M.A.]]
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[[Category: ATP]]
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[[Category: MG]]
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[[Category: alpha-beta fold]]
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[[Category: bent atp conformation]]
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[[Category: magnesium bridge]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:44:37 2007''
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==See Also==
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Aquifex aeolicus]]
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[[Category: Large Structures]]
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[[Category: Schimmel PR]]
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[[Category: Swairjo MA]]

Current revision

crystal structure of alanyl-tRNA synthetase in complex with ATP and magnesium

PDB ID 1yfr

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