1yft: Difference between revisions

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-[[Image:1yft.gif|left|200px]]
- {{Structure
+==The crystal structure of the catalytic fragment of alanyl-tRNA synthetase in complex wtih glycine==
-|PDB= 1yft |SIZE=350|CAPTION= <scene name='initialview01'>1yft</scene>, resolution 2.23&Aring;
+<StructureSection load='1yft' size='340' side='right'caption='[[1yft]], [[Resolution|resolution]] 2.23&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>
+<table><tr><td colspan='2'>[[1yft]] is a 1 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=1YFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YFT FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.23&#8491;</td></tr>
-|GENE= alaS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yft OCA], [https://pdbe.org/1yft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yft RCSB], [https://www.ebi.ac.uk/pdbsum/1yft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yft ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1riq|1RIQ]], [[1yfr|1YFR]], [[1yfs|1YFS]], [[1ygb|1YGB]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yft OCA], [http://www.ebi.ac.uk/pdbsum/1yft PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yft RCSB]</span>
+== Function ==
-}}
+[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]
+== 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/yf/1yft_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=1yft ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-'''The crystal structure of the catalytic fragment of alanyl-tRNA synthetase in complex wtih glycine'''
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1yft" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-YFT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YFT OCA].
+__TOC__
+</StructureSection>
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/15657145 15657145]
-[[Category: Alanine--tRNA ligase]]
 [[Category: Aquifex aeolicus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Schimmel, P R.]]
+[[Category: Schimmel PR]]
-[[Category: Swairjo, M A.]]
+[[Category: Swairjo MA]]
-[[Category: alpha-beta fold]]
-[[Category: amino acid binding]]
-[[Category: helix-loop helix motif]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:05:56 2008''