1tyd: Difference between revisions

Revision as of 16:18, 21 February 2008

STRUCTURE OF TYROSYL-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE

OverviewOverview

The crystal structure of tyrosyl-tRNA synthetase (EC 6.1.1.1) from Bacillus stearothermophilus has been refined to a crystallographic R-factor of 22.6% at 2.3 A resolution using a restrained least-squares procedure. In the final model the root-mean-square deviation from ideality for bond distances is 0.018 A and for angle distances is 0.044 A. Each monomer consists of three domains: an alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet, an alpha-helical domain (248 to 318) containing five helices, and a disordered C-terminal domain (319 to 418) for which the electron density is very weak and where it has not been possible to trace the polypeptide chain. Complexes of the enzyme with the catalytic intermediate tyrosyl adenylate and the inhibitor tyrosinyl adenylate have also been refined to R-factors of 23.9% at 2.8 A resolution and 21.0% at 2.7 A resolution, respectively. Formation of the complexes results in some crystal cracking, but there is no significant difference in the conformation of the polypeptide chain of the three structures described here. The relative orientation of the alpha/beta and alpha-helical domains is similar to that previously observed for the "A" subunit of a deletion mutant lacking the C-terminal domain. Differences between these structures are confined to surface loops that are involved in crystal packing. Tyrosyl adenylate and tyrosinyl adenylate bind in similar conformations within a deep cleft in the alpha/beta domain. The tyrosine moiety is in the equivalent position to that occupied by tyrosine in crystals of the truncated mutant and makes similar strong polar interactions with the enzyme. The alpha-phosphate group interacts with the main-chain nitrogen of Asp38. The two hydroxyl groups of the ribose form strong interactions with the protein. The 2'-hydroxyl group interacts with the carboxylate of Asp194 and the main-chain nitrogen of Gly192 while the 3'-hydroxyl interacts with a tightly bound water molecule (Wat326). The adenine moiety appears to make no significant polar interactions with the protein. The results of site-directed mutagenesis studies are examined in the light of these refined structures.

About this StructureAbout this Structure

1TYD is a Single protein structure of sequence from Geobacillus stearothermophilus with as ligand. Active as Tyrosine--tRNA ligase, with EC number 6.1.1.1 Full crystallographic information is available from OCA.

ReferenceReference

Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate., Brick P, Bhat TN, Blow DM, J Mol Biol. 1989 Jul 5;208(1):83-98. PMID:2504923

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OCA

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-[[Image:1tyd.gif|left|200px]]<br /><applet load="1tyd" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1tyd.gif|left|200px]]<br /><applet load="1tyd" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1tyd, resolution 2.5&Aring;" />
 '''STRUCTURE OF TYROSYL-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE'''<br />
 ==Overview==
-The crystal structure of tyrosyl-tRNA synthetase (EC 6.1.1.1) from, Bacillus stearothermophilus has been refined to a crystallographic, R-factor of 22.6% at 2.3 A resolution using a restrained least-squares, procedure. In the final model the root-mean-square deviation from ideality, for bond distances is 0.018 A and for angle distances is 0.044 A. Each, monomer consists of three domains: an alpha/beta domain (residues 1 to, 220) containing a six-stranded beta-sheet, an alpha-helical domain (248 to, 318) containing five helices, and a disordered C-terminal domain (319 to, 418) for which the electron density is very weak and where it has not been, possible to trace the polypeptide chain. Complexes of the enzyme with the, catalytic intermediate tyrosyl adenylate and the inhibitor tyrosinyl, adenylate have also been refined to R-factors of 23.9% at 2.8 A resolution, and 21.0% at 2.7 A resolution, respectively. Formation of the complexes, results in some crystal cracking, but there is no significant difference, in the conformation of the polypeptide chain of the three structures, described here. The relative orientation of the alpha/beta and, alpha-helical domains is similar to that previously observed for the "A", subunit of a deletion mutant lacking the C-terminal domain. Differences, between these structures are confined to surface loops that are involved, in crystal packing. Tyrosyl adenylate and tyrosinyl adenylate bind in, similar conformations within a deep cleft in the alpha/beta domain. The, tyrosine moiety is in the equivalent position to that occupied by tyrosine, in crystals of the truncated mutant and makes similar strong polar, interactions with the enzyme. The alpha-phosphate group interacts with the, main-chain nitrogen of Asp38. The two hydroxyl groups of the ribose form, strong interactions with the protein. The 2'-hydroxyl group interacts with, the carboxylate of Asp194 and the main-chain nitrogen of Gly192 while the, 3'-hydroxyl interacts with a tightly bound water molecule (Wat326). The, adenine moiety appears to make no significant polar interactions with the, protein. The results of site-directed mutagenesis studies are examined in, the light of these refined structures.
+The crystal structure of tyrosyl-tRNA synthetase (EC 6.1.1.1) from Bacillus stearothermophilus has been refined to a crystallographic R-factor of 22.6% at 2.3 A resolution using a restrained least-squares procedure. In the final model the root-mean-square deviation from ideality for bond distances is 0.018 A and for angle distances is 0.044 A. Each monomer consists of three domains: an alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet, an alpha-helical domain (248 to 318) containing five helices, and a disordered C-terminal domain (319 to 418) for which the electron density is very weak and where it has not been possible to trace the polypeptide chain. Complexes of the enzyme with the catalytic intermediate tyrosyl adenylate and the inhibitor tyrosinyl adenylate have also been refined to R-factors of 23.9% at 2.8 A resolution and 21.0% at 2.7 A resolution, respectively. Formation of the complexes results in some crystal cracking, but there is no significant difference in the conformation of the polypeptide chain of the three structures described here. The relative orientation of the alpha/beta and alpha-helical domains is similar to that previously observed for the "A" subunit of a deletion mutant lacking the C-terminal domain. Differences between these structures are confined to surface loops that are involved in crystal packing. Tyrosyl adenylate and tyrosinyl adenylate bind in similar conformations within a deep cleft in the alpha/beta domain. The tyrosine moiety is in the equivalent position to that occupied by tyrosine in crystals of the truncated mutant and makes similar strong polar interactions with the enzyme. The alpha-phosphate group interacts with the main-chain nitrogen of Asp38. The two hydroxyl groups of the ribose form strong interactions with the protein. The 2'-hydroxyl group interacts with the carboxylate of Asp194 and the main-chain nitrogen of Gly192 while the 3'-hydroxyl interacts with a tightly bound water molecule (Wat326). The adenine moiety appears to make no significant polar interactions with the protein. The results of site-directed mutagenesis studies are examined in the light of these refined structures.
 ==About this Structure==
-TYD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with TYR as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TYD OCA].
+TYD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=TYR:'>TYR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TYD OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Single protein]]
 [[Category: Tyrosine--tRNA ligase]]
-[[Category: Blow, D.M.]]
+[[Category: Blow, D M.]]
-[[Category: Brown, K.A.]]
+[[Category: Brown, K A.]]
-[[Category: Meester, P.De.]]
+[[Category: Meester, P De.]]
 [[Category: TYR]]
 [[Category: aminoacyl-trna synthase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:41:36 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:18:38 2008''