1ggm: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ggm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GGM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GGM FirstGlance]. <br> | <table><tr><td colspan='2'>[[1ggm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GGM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GGM FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAP:GLYCYL-ADENOSINE-5-PHOSPHATE'>GAP</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAP:GLYCYL-ADENOSINE-5-PHOSPHATE'>GAP</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GLYS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GLYS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 Thermus thermophilus HB8])</td></tr> | ||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine--tRNA_ligase Glycine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.14 6.1.1.14] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine--tRNA_ligase Glycine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.14 6.1.1.14] </span></td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ggm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ggm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ggm RCSB], [http://www.ebi.ac.uk/pdbsum/1ggm PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ggm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ggm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ggm RCSB], [http://www.ebi.ac.uk/pdbsum/1ggm PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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[[Category: Glycine--tRNA ligase]] | [[Category: Glycine--tRNA ligase]] | ||
[[Category: Thermus thermophilus hb8]] | [[Category: Thermus thermophilus hb8]] | ||
[[Category: Arnez, J G | [[Category: Arnez, J G]] | ||
[[Category: Moras, D | [[Category: Moras, D]] | ||
[[Category: Aminoacyl-trna synthase]] | [[Category: Aminoacyl-trna synthase]] | ||
[[Category: Ligase]] | [[Category: Ligase]] | ||
Revision as of 22:48, 22 December 2014
GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATEGLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe crystal structures of glycyl-tRNA synthetase (GlyRS) from Thermus thermophilus, a homodimeric class II enzyme, were determined in the enzyme-substrate and enzyme-product states corresponding to the first step of aminoacylation. GlyRS was cocrystallized with glycine and ATP, which were transformed by the enzyme into glycyl-adenylate and thus gave the enzyme-product complex. To trap the enzyme-substrate complex, the enzyme was combined with the glycine analog ethanolamine and ATP. The ligands are bound in fixed orientations in the substrate-binding pocket of the N-terminal active site domain, which contains the classical class II aminoacyl-tRNA synthetase (aaRS) fold. Since glycine does not possess a side-chain, much of the specificity of the enzyme is directed toward excluding any additional atoms beyond the alpha-carbon atom. Several carboxylate residues of GlyRS line the glycine binding pocket; two of them interact directly with the alpha-ammonium group. In addition, the enzyme utilizes the acidic character of the pro-L alpha-hydrogen atom by contacting it via a glutamate carboxylic oxygen atom. A guanidino eta-nitrogen atom of the class II aaRS-conserved motif 2 arginine interacts with the substrate carbonyl oxygen atom. These features serve to attract the small amino acid substrate into the active site and to position it in the correct orientation. GlyRS uses class II-conserved residues to interact with the ATP and the adenosine-phosphate moiety of glycyl-adenylate. On the basis of this similarity, we propose that GlyRS utilizes the same general mechanism as that employed by other class II aminoacyl-tRNA synthetases. Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine.,Arnez JG, Dock-Bregeon AC, Moras D J Mol Biol. 1999 Mar 12;286(5):1449-59. PMID:10064708[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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