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| | <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 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> | + | <table><tr><td colspan='2'>[[5z5e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nanoarchaeum_equitans_Kin4-M Nanoarchaeum equitans 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 [https://proteopedia.org/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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.098Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5z5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z5e OCA], [https://pdbe.org/5z5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z5e RCSB], [https://www.ebi.ac.uk/pdbsum/5z5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z5e ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q74N31_NANEQ Q74N31_NANEQ] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Microarchaeum sp. kin4-m]] | + | [[Category: Nanoarchaeum equitans Kin4-M]] |
| - | [[Category: Noguchi, H]] | + | [[Category: Noguchi H]] |
| - | [[Category: Park, S Y]] | + | [[Category: Park SY]] |
| - | [[Category: Tamura, K]] | + | [[Category: Tamura K]] |
| - | [[Category: Ligase]]
| + | |
| Structural highlights
Function
Q74N31_NANEQ
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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. Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation. 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 doi:http://dx.doi.org/10.1016/j.bbrc.2019.01.142
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