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1n75

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Revision as of 07:04, 7 February 2018

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP.

Structural highlights

1n75 is a 1 chain structure with sequence from "flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1g59, 1gln, 1j09, 1n77, 1n78
Activity:	Glutamate--tRNA ligase, with EC number 6.1.1.17
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[SYE_THET8] Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction: glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu).^[1] ^[2]

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

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.

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^[3]

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

References

↑ Sekine S, Nureki O, Shimada A, Vassylyev DG, Yokoyama S. Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nat Struct Biol. 2001 Mar;8(3):203-6. PMID:11224561 doi:10.1038/84927
↑ Sekine S, Shichiri M, Bernier S, Chenevert R, Lapointe J, Yokoyama S. Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase. Structure. 2006 Dec;14(12):1791-9. PMID:17161369 doi:10.1016/j.str.2006.10.005
↑ Sekine S, Nureki O, Dubois DY, Bernier S, Chenevert R, Lapointe J, Vassylyev DG, Yokoyama S. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J. 2003 Feb 3;22(3):676-88. PMID:12554668 doi:http://dx.doi.org/10.1093/emboj/cdg053

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1n75"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP.==
 <StructureSection load='1n75' size='340' side='right' caption='[[1n75]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1g59|1g59]], [[1gln|1gln]], [[1j09|1j09]], [[1n77|1n77]], [[1n78|1n78]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=1n75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n75 OCA], [http://pdbe.org/1n75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n75 RCSB], [http://www.ebi.ac.uk/pdbsum/1n75 PDBsum], [http://www.topsan.org/Proteins/RSGI/1n75 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=1n75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n75 OCA], [http://pdbe.org/1n75 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n75 RCSB], [http://www.ebi.ac.uk/pdbsum/1n75 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n75 ProSAT], [http://www.topsan.org/Proteins/RSGI/1n75 TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n75_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n75_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 30: @@
 </div>
 <div class="pdbe-citations 1n75" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
 == References ==
 <references/>

1n75

From Proteopedia

Revision as of 07:04, 7 February 2018

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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