1b76
From Proteopedia
(New page: 200px<br /><applet load="1b76" size="450" color="white" frame="true" align="right" spinBox="true" caption="1b76, resolution 3.4Å" /> '''GLYCYL-TRNA SYNTHETAS...) |
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| - | [[Image:1b76.gif|left|200px]]<br /><applet load="1b76" size=" | + | [[Image:1b76.gif|left|200px]]<br /><applet load="1b76" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1b76, resolution 3.4Å" /> | caption="1b76, resolution 3.4Å" /> | ||
'''GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP'''<br /> | '''GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structures of glycyl-tRNA synthetase (GlyRS) from Thermus | + | The 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1B76 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with ATP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http:// | + | 1B76 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B76 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
| - | [[Category: Arnez, J | + | [[Category: Arnez, J G.]] |
[[Category: Moras, D.]] | [[Category: Moras, D.]] | ||
[[Category: ATP]] | [[Category: ATP]] | ||
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[[Category: ligase(synthetase)]] | [[Category: ligase(synthetase)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:52:17 2008'' |
Revision as of 09:52, 21 February 2008
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GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP
Overview
The 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.
About this Structure
1B76 is a Single protein structure of sequence from Thermus thermophilus with as ligand. Active as Glycine--tRNA ligase, with EC number 6.1.1.14 Full crystallographic information is available from OCA.
Reference
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
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