1n78: Difference between revisions

Revision as of 15:03, 21 February 2008

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.

OverviewOverview

Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.

About this StructureAbout this Structure

1N78 is a Single protein structure of sequence from Thermus thermophilus with and as ligands. Active as Glutamate--tRNA ligase, with EC number 6.1.1.17 Full crystallographic information is available from OCA.

ReferenceReference

ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding., Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S, EMBO J. 2003 Feb 3;22(3):676-88. PMID:12554668

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-[[Image:1n78.gif|left|200px]]<br /><applet load="1n78" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1n78.gif|left|200px]]<br /><applet load="1n78" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1n78, resolution 2.10&Aring;" />
 '''Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP.'''<br />
 ==Overview==
-Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from, an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset, of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the, absence of tRNA. In this study, we determined the crystal structure of the, 'non-productive' complex of Thermus thermophilus GluRS, ATP and, L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and, GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of, tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the, ATP-binding site, so that the ATP alpha-phosphate and the glutamate, alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2, A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is, dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but, corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the, 'productive' subsite). Therefore, tRNA binding to GluRS switches the, ATP-binding mode. The interactions of the three tRNA(Glu) regions with, GluRS cause conformational changes around the ATP-binding site, and allow, ATP to bind to the 'productive' subsite.
+Aminoacyl-tRNA synthetases catalyze the formation of an aminoacyl-AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl-tRNA synthetases, including glutamyl-tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl-AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the 'non-productive' complex of Thermus thermophilus GluRS, ATP and L-glutamate, together with those of the GluRS.ATP, GluRS.tRNA.ATP and GluRS.tRNA.GoA (a glutamyl-AMP analog) complexes. In the absence of tRNA(Glu), ATP is accommodated in a 'non-productive' subsite within the ATP-binding site, so that the ATP alpha-phosphate and the glutamate alpha-carboxyl groups in GluRS. ATP.Glu are too far from each other (6.2 A) to react. In contrast, the ATP-binding mode in GluRS.tRNA. ATP is dramatically different from those in GluRS.ATP.Glu and GluRS.ATP, but corresponds to the AMP moiety binding mode in GluRS.tRNA.GoA (the 'productive' subsite). Therefore, tRNA binding to GluRS switches the ATP-binding mode. The interactions of the three tRNA(Glu) regions with GluRS cause conformational changes around the ATP-binding site, and allow ATP to bind to the 'productive' subsite.
 ==About this Structure==
-N78 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 MG and GOM as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N78 OCA].
+N78 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=MG:'>MG</scene> and <scene name='pdbligand=GOM:'>GOM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutamate--tRNA_ligase Glutamate--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.17 6.1.1.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N78 OCA].
 ==Reference==
@@ Line 16: / Line 16: @@
 [[Category: Bernier, S.]]
 [[Category: Chenevert, R.]]
-[[Category: Dubois, D.Y.]]
+[[Category: Dubois, D Y.]]
 [[Category: Lapointe, J.]]
 [[Category: Nureki, O.]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
 [[Category: Sekine, S.]]
-[[Category: Vassylyev, D.G.]]
+[[Category: Vassylyev, D G.]]
 [[Category: Yokoyama, S.]]
 [[Category: GOM]]
@@ Line 30: / Line 30: @@
 [[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:01:01 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:03:01 2008''