3rl6: Difference between revisions

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 ==Crystal structure of the archaeal asparagine synthetase A complexed with L-Asparagine and Adenosine monophosphate==
-<StructureSection load='3rl6' size='340' side='right' caption='[[3rl6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3rl6' size='340' side='right'caption='[[3rl6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3rl6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RL6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3rl6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RL6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RL6 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
+</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&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">asnS-like, PYRAB02460, PAB2356 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rl6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rl6 RCSB], [http://www.ebi.ac.uk/pdbsum/3rl6 PDBsum]</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=3rl6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rl6 OCA], [https://pdbe.org/3rl6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rl6 RCSB], [https://www.ebi.ac.uk/pdbsum/3rl6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rl6 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.
-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>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus abyssi]]
+[[Category: Large Structures]]
-[[Category: Blaise, M.]]
+[[Category: Pyrococcus abyssi GE5]]
-[[Category: Charron, C.]]
+[[Category: Blaise M]]
-[[Category: Frechin, M.]]
+[[Category: Charron C]]
-[[Category: Kern, D.]]
+[[Category: Frechin M]]
-[[Category: Lorber, B.]]
+[[Category: Kern D]]
-[[Category: Olieric, V.]]
+[[Category: Lorber B]]
-[[Category: Roy, H.]]
+[[Category: Olieric V]]
-[[Category: Sauter, C.]]
+[[Category: Roy H]]
-[[Category: Amp and asn binding]]
+[[Category: Sauter C]]
-[[Category: Ligase]]
-[[Category: Seven stranded antiparallel beta-sheet]]