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3akz

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Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with tRNAGln and a glutamyl-AMP analog

Structural highlights

3akz is a 8 chain structure with sequence from Thermotoga maritima and Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYE2_THEMA 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).[HAMAP-Rule:MF_00022]

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

In most bacteria and all archaea, glutamyl-tRNA synthetase (GluRS) glutamylates both tRNA(Glu) and tRNA(Gln), and then Glu-tRNA(Gln) is selectively converted to Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. The mechanisms by which the two enzymes recognize their substrate tRNA(s), and how they cooperate with each other in Gln-tRNA(Gln) synthesis, remain to be determined. Here we report the formation of the 'glutamine transamidosome' from the bacterium Thermotoga maritima, consisting of tRNA(Gln), GluRS and the heterotrimeric amidotransferase GatCAB, and its crystal structure at 3.35 A resolution. The anticodon-binding body of GluRS recognizes the common features of tRNA(Gln) and tRNA(Glu), whereas the tail body of GatCAB recognizes the outer corner of the L-shaped tRNA(Gln) in a tRNA(Gln)-specific manner. GluRS is in the productive form, as its catalytic body binds to the amino-acid-acceptor arm of tRNA(Gln). In contrast, GatCAB is in the non-productive form: the catalytic body of GatCAB contacts that of GluRS and is located near the acceptor stem of tRNA(Gln), in an appropriate site to wait for the completion of Glu-tRNA(Gln) formation by GluRS. We identified the hinges between the catalytic and anticodon-binding bodies of GluRS and between the catalytic and tail bodies of GatCAB, which allow both GluRS and GatCAB to adopt the productive and non-productive forms. The catalytic bodies of the two enzymes compete for the acceptor arm of tRNA(Gln) and therefore cannot assume their productive forms simultaneously. The transition from the present glutamylation state, with the productive GluRS and the non-productive GatCAB, to the putative amidation state, with the non-productive GluRS and the productive GatCAB, requires an intermediate state with the two enzymes in their non-productive forms, for steric reasons. The proposed mechanism explains how the transamidosome efficiently performs the two consecutive steps of Gln-tRNA(Gln) formation, with a low risk of releasing the unstable intermediate Glu-tRNA(Gln).

Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions.,Ito T, Yokoyama S Nature. 2010 Sep 30;467(7315):612-6. PMID:20882017^[1]

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

References

↑ Ito T, Yokoyama S. Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions. Nature. 2010 Sep 30;467(7315):612-6. PMID:20882017 doi:10.1038/nature09411

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/3akz"

Categories: Large Structures | Thermotoga maritima | Thermotoga maritima MSB8 | Ito T | Yokoyama S

@@ Line 1: / Line 1: @@
 ==Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with tRNAGln and a glutamyl-AMP analog==
-<StructureSection load='3akz' size='340' side='right' caption='[[3akz]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='3akz' size='340' side='right'caption='[[3akz]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3akz]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AKZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AKZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3akz]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] and [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AKZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GSU:O5-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE'>GSU</scene></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]] 2.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3al0|3al0]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GSU:O5-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE'>GSU</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gltX2, TM_1875 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=3akz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3akz OCA], [https://pdbe.org/3akz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3akz RCSB], [https://www.ebi.ac.uk/pdbsum/3akz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3akz ProSAT]</span></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=3akz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3akz OCA], [http://pdbe.org/3akz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3akz RCSB], [http://www.ebi.ac.uk/pdbsum/3akz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3akz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SYE2_THEMA SYE2_THEMA]] 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).[HAMAP-Rule:MF_00022]
+[https://www.uniprot.org/uniprot/SYE2_THEMA SYE2_THEMA] 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).[HAMAP-Rule:MF_00022]
 == 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/ak/3akz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ak/3akz_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 31: @@
 ==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-*[[TRNA|TRNA]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Glutamate--tRNA ligase]]
+[[Category: Large Structures]]
-[[Category: Thema]]
+[[Category: Thermotoga maritima]]
-[[Category: Ito, T]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Yokoyama, S]]
+[[Category: Ito T]]
-[[Category: Ligase-rna complex]]
+[[Category: Yokoyama S]]
-[[Category: Protein-rna complex]]

3akz

From Proteopedia

Current revision

Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with tRNAGln and a glutamyl-AMP analog

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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