1iq0: Difference between revisions

Revision as of 14:14, 21 February 2008

THERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE

OverviewOverview

Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNA(Arg): A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNA(Arg). In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from Thermus thermophilus at 2.3 A resolution. The structure of the T. thermophilus ArgRS was found to be similar to that of the previously reported S. cerevisiae ArgRS, except for short insertions and a concomitant conformational change in the N-terminal domain. The structure of the yeast ArgRS.tRNA(Arg) complex suggested that two residues in the unique N-terminal domain, Tyr(77) and Asn(79), which are phylogenetically invariant in the ArgRSs from all organisms with A20 in tRNA(Arg)s, are involved in A20 recognition. However, in a docking model constructed based on the yeast ArgRS.tRNA(Arg) and T. thermophilus ArgRS structures, Tyr(77) and Asn(79) are not close enough to make direct contact with A20, because of the conformational change in the N-terminal domain. Nevertheless, the replacement of Tyr(77) or Asn(79) by Ala severely reduced the arginylation efficiency. Therefore, some conformational change around A20 is necessary for the recognition. Surprisingly, the N79D mutant equally recognized A20 and G20, with only a slight reduction in the arginylation efficiency as compared with the wild-type enzyme. Other mutants of Asn(79) also exhibited broader specificity for the nucleotide at position 20 of tRNA(Arg). We propose a model of A20 recognition by the ArgRS that is consistent with the present results of the mutational analyses.

About this StructureAbout this Structure

1IQ0 is a Single protein structure of sequence from Thermus thermophilus. Active as Arginine--tRNA ligase, with EC number 6.1.1.19 Full crystallographic information is available from OCA.

ReferenceReference

Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase., Shimada A, Nureki O, Goto M, Takahashi S, Yokoyama S, Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13537-42. Epub 2001 Nov 6. PMID:11698642

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-[[Image:1iq0.jpg|left|200px]]<br /><applet load="1iq0" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1iq0.jpg|left|200px]]<br /><applet load="1iq0" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1iq0, resolution 2.30&Aring;" />
 '''THERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE'''<br />
 ==Overview==
-Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of, tRNA(Arg): A20, located at the outside corner of the L-shaped tRNA, and, C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNA(Arg). In the, present study, we solved the crystal structure of a typical, A20-recognizing ArgRS from Thermus thermophilus at 2.3 A resolution. The, structure of the T. thermophilus ArgRS was found to be similar to that of, the previously reported S. cerevisiae ArgRS, except for short insertions, and a concomitant conformational change in the N-terminal domain. The, structure of the yeast ArgRS.tRNA(Arg) complex suggested that two residues, in the unique N-terminal domain, Tyr(77) and Asn(79), which are, phylogenetically invariant in the ArgRSs from all organisms with A20 in, tRNA(Arg)s, are involved in A20 recognition. However, in a docking model, constructed based on the yeast ArgRS.tRNA(Arg) and T. thermophilus ArgRS, structures, Tyr(77) and Asn(79) are not close enough to make direct, contact with A20, because of the conformational change in the N-terminal, domain. Nevertheless, the replacement of Tyr(77) or Asn(79) by Ala, severely reduced the arginylation efficiency. Therefore, some, conformational change around A20 is necessary for the recognition., Surprisingly, the N79D mutant equally recognized A20 and G20, with only a, slight reduction in the arginylation efficiency as compared with the, wild-type enzyme. Other mutants of Asn(79) also exhibited broader, specificity for the nucleotide at position 20 of tRNA(Arg). We propose a, model of A20 recognition by the ArgRS that is consistent with the present, results of the mutational analyses.
+Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNA(Arg): A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNA(Arg). In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from Thermus thermophilus at 2.3 A resolution. The structure of the T. thermophilus ArgRS was found to be similar to that of the previously reported S. cerevisiae ArgRS, except for short insertions and a concomitant conformational change in the N-terminal domain. The structure of the yeast ArgRS.tRNA(Arg) complex suggested that two residues in the unique N-terminal domain, Tyr(77) and Asn(79), which are phylogenetically invariant in the ArgRSs from all organisms with A20 in tRNA(Arg)s, are involved in A20 recognition. However, in a docking model constructed based on the yeast ArgRS.tRNA(Arg) and T. thermophilus ArgRS structures, Tyr(77) and Asn(79) are not close enough to make direct contact with A20, because of the conformational change in the N-terminal domain. Nevertheless, the replacement of Tyr(77) or Asn(79) by Ala severely reduced the arginylation efficiency. Therefore, some conformational change around A20 is necessary for the recognition. Surprisingly, the N79D mutant equally recognized A20 and G20, with only a slight reduction in the arginylation efficiency as compared with the wild-type enzyme. Other mutants of Asn(79) also exhibited broader specificity for the nucleotide at position 20 of tRNA(Arg). We propose a model of A20 recognition by the ArgRS that is consistent with the present results of the mutational analyses.
 ==About this Structure==
-IQ0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Active as [http://en.wikipedia.org/wiki/Arginine--tRNA_ligase Arginine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.19 6.1.1.19] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IQ0 OCA].
+IQ0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Active as [http://en.wikipedia.org/wiki/Arginine--tRNA_ligase Arginine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.19 6.1.1.19] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQ0 OCA].
 ==Reference==
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 [[Category: Goto, M.]]
 [[Category: Nureki, O.]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
 [[Category: Shimada, A.]]
 [[Category: Takahashi, S.]]
@@ Line 25: / Line 25: @@
 [[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:21:12 2007''
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