5z5e
From Proteopedia
(Difference between revisions)
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==Crystal structure of the Glycyl-tRNA synthetase (GlyRS) in Nanoarchaeum equitans== | ==Crystal structure of the Glycyl-tRNA synthetase (GlyRS) in Nanoarchaeum equitans== | ||
| - | <StructureSection load='5z5e' size='340' side='right' caption='[[5z5e]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='5z5e' size='340' side='right'caption='[[5z5e]], [[Resolution|resolution]] 2.10Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5z5e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5E FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5z5e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Microarchaeum_sp._kin4-m Microarchaeum sp. kin4-m]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z5E FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NEQ417 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=228908 Microarchaeum sp. Kin4-M])</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=5z5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5e OCA], [http://pdbe.org/5z5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5e RCSB], [http://www.ebi.ac.uk/pdbsum/5z5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5e ProSAT]</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=5z5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5e OCA], [http://pdbe.org/5z5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z5e RCSB], [http://www.ebi.ac.uk/pdbsum/5z5e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5e ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | This study reports the X-ray crystallographic structure of the glycyl-tRNA synthetase (GlyRS) of Nanoarchaeum equitans - a hyperthermophilic archaeal species. This is the first archaeal GlyRS crystal structure elucidated. The GlyRS comprises an N-terminal catalytic domain and a C-terminal anticodon-binding domain with a long beta-sheet inserted between these domains. An unmodified transcript of the wild-type N. equitans tRNA(Gly) was successfully glycylated using GlyRS. Substitution of the discriminator base A73 of tRNA(Gly) with any other nucleotide caused a significant decrease in glycylation activity. Mutational analysis of the second base-pair C2G71 of the acceptor stem of tRNA(Gly) elucidated the importance of the base-pair, especially G71, as an identity element for recognition by GlyRS. Glycylation assays using tRNA(Gly) G71 substitution mutants and a GlyRS mutant where Arg223 is mutated to alanine strengthen the possibility that the carbonyl oxygen at position 6 of G71 would hydrogen-bond with the guanidine nitrogen of Arg223 in N. equitans GlyRS. | ||
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| + | Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation.,Fujisawa A, Toki R, Miyake H, Shoji T, Doi H, Hayashi H, Hanabusa R, Mutsuro-Aoki H, Umehara T, Ando T, Noguchi H, Voet A, Park SY, Tamura K Biochem Biophys Res Commun. 2019 Apr 2;511(2):228-233. doi:, 10.1016/j.bbrc.2019.01.142. Epub 2019 Feb 13. PMID:30771900<ref>PMID:30771900</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5z5e" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Microarchaeum sp. kin4-m]] | ||
[[Category: Noguchi, H]] | [[Category: Noguchi, H]] | ||
[[Category: Park, S Y]] | [[Category: Park, S Y]] | ||
[[Category: Tamura, K]] | [[Category: Tamura, K]] | ||
[[Category: Ligase]] | [[Category: Ligase]] | ||
Revision as of 06:24, 21 August 2019
Crystal structure of the Glycyl-tRNA synthetase (GlyRS) in Nanoarchaeum equitans
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