1nyr
From Proteopedia
(New page: 200px<br /><applet load="1nyr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nyr, resolution 2.80Å" /> '''Structure of Staphyl...) |
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| - | [[Image:1nyr.gif|left|200px]]<br /><applet load="1nyr" size=" | + | [[Image:1nyr.gif|left|200px]]<br /><applet load="1nyr" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1nyr, resolution 2.80Å" /> | caption="1nyr, resolution 2.80Å" /> | ||
'''Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP'''<br /> | '''Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structures of threonyl-tRNA synthetase (ThrRS) from | + | The crystal structures of threonyl-tRNA synthetase (ThrRS) from Staphylococcus aureus, with ATP and an analogue of threonyl adenylate, are described. Together with the previously determined structures of Escherichia coli ThrRS with different substrates, they allow a comprehensive analysis of the effect of binding of all the substrates: threonine, ATP and tRNA. The tRNA, by inserting its acceptor arm between the N-terminal domain and the catalytic domain, causes a large rotation of the former. Within the catalytic domain, four regions surrounding the active site display significant conformational changes upon binding of the different substrates. The binding of threonine induces the movement of as much as 50 consecutive amino acid residues. The binding of ATP triggers a displacement, as large as 8A at some C(alpha) positions, of a strand-loop-strand region of the core beta-sheet. Two other regions move in a cooperative way upon binding of threonine or ATP: the motif 2 loop, which plays an essential role in the first step of the aminoacylation reaction, and the ordering loop, which closes on the active site cavity when the substrates are in place. The tRNA interacts with all four mobile regions, several residues initially bound to threonine or ATP switching to a position in which they can contact the tRNA. Three such conformational switches could be identified, each of them in a different mobile region. The structural analysis suggests that, while the small substrates can bind in any order, they must be in place before productive tRNA binding can occur. |
==About this Structure== | ==About this Structure== | ||
| - | 1NYR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] with ZN, ATP and THR as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] Full crystallographic information is available from [http:// | + | 1NYR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=ATP:'>ATP</scene> and <scene name='pdbligand=THR:'>THR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Threonine--tRNA_ligase Threonine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.3 6.1.1.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NYR OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Staphylococcus aureus]] | [[Category: Staphylococcus aureus]] | ||
[[Category: Threonine--tRNA ligase]] | [[Category: Threonine--tRNA ligase]] | ||
| - | [[Category: Dock-Bregeon, A | + | [[Category: Dock-Bregeon, A C.]] |
[[Category: Moras, D.]] | [[Category: Moras, D.]] | ||
[[Category: Rees, B.]] | [[Category: Rees, B.]] | ||
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[[Category: threonyl-trna synthetase]] | [[Category: threonyl-trna synthetase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:11:31 2008'' |
Revision as of 12:11, 21 February 2008
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Structure of Staphylococcus aureus threonyl-tRNA synthetase complexed with ATP
Overview
The crystal structures of threonyl-tRNA synthetase (ThrRS) from Staphylococcus aureus, with ATP and an analogue of threonyl adenylate, are described. Together with the previously determined structures of Escherichia coli ThrRS with different substrates, they allow a comprehensive analysis of the effect of binding of all the substrates: threonine, ATP and tRNA. The tRNA, by inserting its acceptor arm between the N-terminal domain and the catalytic domain, causes a large rotation of the former. Within the catalytic domain, four regions surrounding the active site display significant conformational changes upon binding of the different substrates. The binding of threonine induces the movement of as much as 50 consecutive amino acid residues. The binding of ATP triggers a displacement, as large as 8A at some C(alpha) positions, of a strand-loop-strand region of the core beta-sheet. Two other regions move in a cooperative way upon binding of threonine or ATP: the motif 2 loop, which plays an essential role in the first step of the aminoacylation reaction, and the ordering loop, which closes on the active site cavity when the substrates are in place. The tRNA interacts with all four mobile regions, several residues initially bound to threonine or ATP switching to a position in which they can contact the tRNA. Three such conformational switches could be identified, each of them in a different mobile region. The structural analysis suggests that, while the small substrates can bind in any order, they must be in place before productive tRNA binding can occur.
About this Structure
1NYR is a Single protein structure of sequence from Staphylococcus aureus with , and as ligands. Active as Threonine--tRNA ligase, with EC number 6.1.1.3 Full crystallographic information is available from OCA.
Reference
Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase., Torres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D, J Mol Biol. 2003 Aug 1;331(1):201-11. PMID:12875846
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