|
|
| Line 3: |
Line 3: |
| | <StructureSection load='5gro' size='340' side='right'caption='[[5gro]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='5gro' size='340' side='right'caption='[[5gro]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gro]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GRO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gro]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GRO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</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]] 2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aspS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate--tRNA(Asn)_ligase Aspartate--tRNA(Asn) ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.23 6.1.1.23] </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=5gro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gro OCA], [https://pdbe.org/5gro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gro RCSB], [https://www.ebi.ac.uk/pdbsum/5gro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gro ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gro OCA], [http://pdbe.org/5gro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gro RCSB], [http://www.ebi.ac.uk/pdbsum/5gro PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gro ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SYDND_HELPY SYDND_HELPY]] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over tRNA(Asn). Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).<ref>PMID:16800632</ref> | + | [https://www.uniprot.org/uniprot/SYDND_HELPY SYDND_HELPY] Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over tRNA(Asn). Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).<ref>PMID:16800632</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 27: |
Line 26: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Campylobacter pylori]] | + | [[Category: Helicobacter pylori 26695]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Chen, C J]] | + | [[Category: Chen C-J]] |
| - | [[Category: Chuawong, P]] | + | [[Category: Chuawong P]] |
| - | [[Category: Fuengfuloy, P]] | + | [[Category: Fuengfuloy P]] |
| - | [[Category: Songsiriritthigul, C]] | + | [[Category: Songsiriritthigul C]] |
| - | [[Category: Suebka, S]] | + | [[Category: Suebka S]] |
| - | [[Category: Anticodon-binding domain]]
| + | |
| - | [[Category: Helicobacter pylori]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Non-discriminating aspartyl-trna synthetase]]
| + | |
| Structural highlights
Function
SYDND_HELPY Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Is 1.7 times more efficient at aminoacylating tRNA(Asp) over tRNA(Asn). Reaction proceeds in two steps: aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp/Asn).[1]
Publication Abstract from PubMed
The N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) plays a crucial role in the recognition of both tRNAAsp and tRNAAsn. Here, the first X-ray crystal structure of the N-terminal domain of this enzyme (ND-AspRS1-104) from the human-pathogenic bacterium Helicobacter pylori is reported at 2.0 A resolution. The apo form of H. pylori ND-AspRS1-104 shares high structural similarity with the N-terminal anticodon-binding domains of the discriminating aspartyl-tRNA synthetase (D-AspRS) from Escherichia coli and ND-AspRS from Pseudomonas aeruginosa, allowing recognition elements to be proposed for tRNAAsp and tRNAAsn. It is proposed that a long loop (Arg77-Lys90) in this H. pylori domain influences its relaxed tRNA specificity, such that it is classified as nondiscriminating. A structural comparison between D-AspRS from E. coli and ND-AspRS from P. aeruginosa suggests that turns E and F (78GAGL81 and 83NPKL86) in H. pylori ND-AspRS play a crucial role in anticodon recognition. Accordingly, the conserved Pro84 in turn F facilitates the recognition of the anticodons of tRNAAsp (34GUC36) and tRNAAsn (34GUU36). The absence of the amide H atom allows both C and U bases to be accommodated in the tRNA-recognition site.
Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori.,Songsiriritthigul C, Suebka S, Chen CJ, Fuengfuloy P, Chuawong P Acta Crystallogr F Struct Biol Commun. 2017 Feb 1;73(Pt 2):62-69. doi:, 10.1107/S2053230X16020586. Epub 2017 Jan 19. PMID:28177315[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Chuawong P, Hendrickson TL. The nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori: anticodon-binding domain mutations that impact tRNA specificity and heterologous toxicity. Biochemistry. 2006 Jul 4;45(26):8079-87. PMID:16800632 doi:http://dx.doi.org/10.1021/bi060189c
- ↑ Songsiriritthigul C, Suebka S, Chen CJ, Fuengfuloy P, Chuawong P. Crystal structure of the N-terminal anticodon-binding domain of the nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori. Acta Crystallogr F Struct Biol Commun. 2017 Feb 1;73(Pt 2):62-69. doi:, 10.1107/S2053230X16020586. Epub 2017 Jan 19. PMID:28177315 doi:http://dx.doi.org/10.1107/S2053230X16020586
|
