1o0b: Difference between revisions

Revision as of 15:11, 21 February 2008

CRYSTAL STRUCTURE OF L-GLUTAMINE AND AMPCPP BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE

OverviewOverview

The 2.5 A crystal structure of Escherichia coli glutaminyl-tRNA synthetase in a quaternary complex with tRNA(Gln), an ATP analog and glutamate reveals that the non-cognate amino acid adopts a distinct binding mode within the active site cleft. In contrast to the binding of cognate glutamine, one oxygen of the charged glutamate carboxylate group makes a direct ion-pair interaction with the strictly conserved Arg30 residue located in the first half of the dinucleotide fold domain. The nucleophilic alpha-carboxylate moiety of glutamate is mispositioned with respect to both the ATP alpha-phosphate and terminal tRNA ribose groups, suggesting that a component of amino acid discrimination resides at the catalytic step of the reaction. Further, the other side-chain carboxylate oxygen of glutamate is found in a position identical to that previously proposed to be occupied by the NH(2) group of the cognate glutamine substrate. At this position, the glutamate oxygen accepts hydrogen bonds from the hydroxyl moiety of Tyr211 and a water molecule. These findings demonstrate that amino acid specificity by GlnRS cannot arise from hydrogen bonds donated by the cognate glutamine amide to these same moieties, as previously suggested. Instead, Arg30 functions as a negative determinant to drive binding of non-cognate glutamate into a non-productive orientation. The poorly differentiated cognate amino acid-binding site in GlnRS may be a consequence of the late emergence of this enzyme from the eukaryotic lineage of glutamyl-tRNA synthetases.

About this StructureAbout this Structure

1O0B is a Protein complex structure of sequences from Escherichia coli with , and as ligands. Active as Glutamine--tRNA ligase, with EC number 6.1.1.18 Full crystallographic information is available from OCA.

ReferenceReference

Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants., Bullock TL, Uter N, Nissan TA, Perona JJ, J Mol Biol. 2003 Apr 25;328(2):395-408. PMID:12691748

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-[[Image:1o0b.gif|left|200px]]<br /><applet load="1o0b" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1o0b, resolution 2.70&Aring;" />
 '''CRYSTAL STRUCTURE OF L-GLUTAMINE AND AMPCPP BOUND TO GLUTAMINE AMINOACYL TRNA SYNTHETASE'''<br />
 ==Overview==
-The 2.5 A crystal structure of Escherichia coli glutaminyl-tRNA synthetase, in a quaternary complex with tRNA(Gln), an ATP analog and glutamate, reveals that the non-cognate amino acid adopts a distinct binding mode, within the active site cleft. In contrast to the binding of cognate, glutamine, one oxygen of the charged glutamate carboxylate group makes a, direct ion-pair interaction with the strictly conserved Arg30 residue, located in the first half of the dinucleotide fold domain. The, nucleophilic alpha-carboxylate moiety of glutamate is mispositioned with, respect to both the ATP alpha-phosphate and terminal tRNA ribose groups, suggesting that a component of amino acid discrimination resides at the, catalytic step of the reaction. Further, the other side-chain carboxylate, oxygen of glutamate is found in a position identical to that previously, proposed to be occupied by the NH(2) group of the cognate glutamine, substrate. At this position, the glutamate oxygen accepts hydrogen bonds, from the hydroxyl moiety of Tyr211 and a water molecule. These findings, demonstrate that amino acid specificity by GlnRS cannot arise from, hydrogen bonds donated by the cognate glutamine amide to these same, moieties, as previously suggested. Instead, Arg30 functions as a negative, determinant to drive binding of non-cognate glutamate into a, non-productive orientation. The poorly differentiated cognate amino, acid-binding site in GlnRS may be a consequence of the late emergence of, this enzyme from the eukaryotic lineage of glutamyl-tRNA synthetases.
+The 2.5 A crystal structure of Escherichia coli glutaminyl-tRNA synthetase in a quaternary complex with tRNA(Gln), an ATP analog and glutamate reveals that the non-cognate amino acid adopts a distinct binding mode within the active site cleft. In contrast to the binding of cognate glutamine, one oxygen of the charged glutamate carboxylate group makes a direct ion-pair interaction with the strictly conserved Arg30 residue located in the first half of the dinucleotide fold domain. The nucleophilic alpha-carboxylate moiety of glutamate is mispositioned with respect to both the ATP alpha-phosphate and terminal tRNA ribose groups, suggesting that a component of amino acid discrimination resides at the catalytic step of the reaction. Further, the other side-chain carboxylate oxygen of glutamate is found in a position identical to that previously proposed to be occupied by the NH(2) group of the cognate glutamine substrate. At this position, the glutamate oxygen accepts hydrogen bonds from the hydroxyl moiety of Tyr211 and a water molecule. These findings demonstrate that amino acid specificity by GlnRS cannot arise from hydrogen bonds donated by the cognate glutamine amide to these same moieties, as previously suggested. Instead, Arg30 functions as a negative determinant to drive binding of non-cognate glutamate into a non-productive orientation. The poorly differentiated cognate amino acid-binding site in GlnRS may be a consequence of the late emergence of this enzyme from the eukaryotic lineage of glutamyl-tRNA synthetases.
 ==About this Structure==
-O0B is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with SO4, GLN and AMP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1O0B OCA].
+O0B is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=GLN:'>GLN</scene> and <scene name='pdbligand=AMP:'>AMP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutamine--tRNA_ligase Glutamine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.18 6.1.1.18] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O0B OCA].
 ==Reference==
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 [[Category: Glutamine--tRNA ligase]]
 [[Category: Protein complex]]
-[[Category: Bullock, T.L.]]
+[[Category: Bullock, T L.]]
-[[Category: Perona, J.J.]]
+[[Category: Perona, J J.]]
 [[Category: AMP]]
 [[Category: GLN]]
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 [[Category: trna-protein complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:42:12 2007''
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