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| | <StructureSection load='3p8v' size='340' side='right'caption='[[3p8v]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='3p8v' size='340' side='right'caption='[[3p8v]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P8V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3p8v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P8V FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3p8t|3p8t]], [[3p8y|3p8y]], [[3reu|3reu]], [[3rex|3rex]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [https://pdbe.org/3p8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [https://www.ebi.ac.uk/pdbsum/3p8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8v 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=3p8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p8v OCA], [https://pdbe.org/3p8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p8v RCSB], [https://www.ebi.ac.uk/pdbsum/3p8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p8v ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q9V228_PYRAB Q9V228_PYRAB] |
| - | Asparagine synthetase A (AsnA) catalyzes asparagine synthesis using aspartate, ATP, and ammonia as substrates. Asparagine is formed in two steps: the beta-carboxylate group of aspartate is first activated by ATP to form an aminoacyl-AMP before its amidation by a nucleophilic attack with an ammonium ion. Interestingly, this mechanism of amino acid activation resembles that used by aminoacyl-tRNA synthetases, which first activate the alpha-carboxylate group of the amino acid to form also an aminoacyl-AMP before they transfer the activated amino acid onto the cognate tRNA. In a previous investigation, we have shown that the open reading frame of Pyrococcus abyssi annotated as asparaginyl-tRNA synthetase (AsnRS) 2 is, in fact, an archaeal asparagine synthetase A (AS-AR) that evolved from an ancestral aspartyl-tRNA synthetase (AspRS). We present here the crystal structure of this AS-AR. The fold of this protein is similar to that of bacterial AsnA and resembles the catalytic cores of AspRS and AsnRS. The high-resolution structures of AS-AR associated with its substrates and end-products help to understand the reaction mechanism of asparagine formation and release. A comparison of the catalytic core of AS-AR with those of archaeal AspRS and AsnRS and with that of bacterial AsnA reveals a strong conservation. This study uncovers how the active site of the ancestral AspRS rearranged throughout evolution to transform an enzyme activating the alpha-carboxylate group into an enzyme that is able to activate the beta-carboxylate group of aspartate, which can react with ammonia instead of tRNA.
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| - | Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.,Blaise M, Frechin M, Olieric V, Charron C, Sauter C, Lorber B, Roy H, Kern D J Mol Biol. 2011 Sep 23;412(3):437-52. Epub 2011 Jul 28. PMID:21820443<ref>PMID:21820443</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
| + | |
| - | <div class="pdbe-citations 3p8v" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrococcus abyssi erauso et al. 1993]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Blaise, M]] | + | [[Category: Pyrococcus abyssi]] |
| - | [[Category: Kern, D]] | + | [[Category: Blaise M]] |
| - | [[Category: Ammonium]] | + | [[Category: Kern D]] |
| - | [[Category: Amp]]
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| - | [[Category: Anti-parallel beta sheet]]
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| - | [[Category: Asn]]
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| - | [[Category: Asp]]
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| - | [[Category: Asparagine synthetase]]
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| - | [[Category: Atp binding]]
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| - | [[Category: Ligase]]
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| - | [[Category: Synthetase]]
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