1iq0

From Proteopedia

(Difference between revisions)

Current revision

THERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE

Structural highlights

1iq0 is a 1 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

Q93RP5_THETH

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shimada A, Nureki O, Goto M, Takahashi S, Yokoyama S. Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase. Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13537-42. Epub 2001 Nov 6. PMID:11698642 doi:10.1073/pnas.231267998

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1iq0"

@@ Line 1: / Line 1: @@
 ==THERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE==
-<StructureSection load='1iq0' size='340' side='right' caption='[[1iq0]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1iq0' size='340' side='right'caption='[[1iq0]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1iq0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IQ0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1iq0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IQ0 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARGS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iq0 OCA], [https://pdbe.org/1iq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iq0 RCSB], [https://www.ebi.ac.uk/pdbsum/1iq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iq0 ProSAT], [https://www.topsan.org/Proteins/RSGI/1iq0 TOPSAN]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iq0 OCA], [http://pdbe.org/1iq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iq0 RCSB], [http://www.ebi.ac.uk/pdbsum/1iq0 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iq0 TOPSAN]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q93RP5_THETH Q93RP5_THETH]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iq/1iq0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iq/1iq0_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1iq0 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 30: @@
 ==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
+[[Category: Large Structures]]
-[[Category: Arginine--tRNA ligase]]
+[[Category: Thermus thermophilus]]
-[[Category: Goto, M]]
+[[Category: Goto M]]
-[[Category: Nureki, O]]
+[[Category: Nureki O]]
-[[Category: Structural genomic]]
+[[Category: Shimada A]]
-[[Category: Shimada, A]]
+[[Category: Takahashi S]]
-[[Category: Takahashi, S]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S]]
-[[Category: Arginyl-trna synthetase]]
-[[Category: Ligase]]
-[[Category: Rsgi]]

1iq0

From Proteopedia

Current revision

THERMUS THERMOPHILUS ARGINYL-TRNA SYNTHETASE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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