5yge: Difference between revisions

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 ==ArgA complexed with AceCoA and glutamate==
-<StructureSection load='5yge' size='340' side='right' caption='[[5yge]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
+<StructureSection load='5yge' size='340' side='right'caption='[[5yge]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5yge]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YGE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5yge]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YGE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=CAD:CACODYLIC+ACID'>CAD</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</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]] 2.039&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">argA, Rv2747 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</scene>, <scene name='pdbligand=CAD:CACODYLIC+ACID'>CAD</scene>, <scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Amino-acid_N-acetyltransferase Amino-acid N-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.1 2.3.1.1] </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=5yge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yge OCA], [https://pdbe.org/5yge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yge RCSB], [https://www.ebi.ac.uk/pdbsum/5yge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yge 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=5yge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yge OCA], [http://pdbe.org/5yge PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yge RCSB], [http://www.ebi.ac.uk/pdbsum/5yge PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yge ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ARGA_MYCTU ARGA_MYCTU]] Catalyzes the conversion of L-glutamate to alpha-N-acetyl-L-glutamate. L-glutamine is a significantly better substrate compared to L-glutamate.<ref>PMID:15838030</ref>
+[https://www.uniprot.org/uniprot/ARGA_MYCTU ARGA_MYCTU] Catalyzes the conversion of L-glutamate to alpha-N-acetyl-L-glutamate. L-glutamine is a significantly better substrate compared to L-glutamate.<ref>PMID:15838030</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-l-arginine is used as a source of both carbon and nitrogen in Mycobacterium tuberculosis (Mtb) and its biosynthesis is essential for the pathogen's survival. MtbArgA (Rv2747) catalyzes the initial step in l-arginine biosynthesis by transferring an acetyl group from acetyl coenzyme A (AcCoA) to l-glutamate. MtbArgA is a class III N-acetylglutamate synthase (NAGS) with no structural information. Here, we solved the crystal structure of MtbArgA complexed with AcCoA and l-glutamate. The overall structure adopts a classic fold of the GCN5-related N-acetyltransferase (GNAT) family, characterized by a "V"-shaped cleft and beta-bulge, but uses distinct residues for the binding and reaction of AcCoA. In particular, its activity depends on dimerization to form a deep, vast pocket for l-glutamate binding. Interestingly, in the structure, l-glutamate binds at a site far away from AcCoA, implying a mechanism of separate capture and catalysis. Additionally, based on a docking model of l-glutamate at the catalytic site, a one-step sequential mechanism was proposed for enzymatic catalysis. Important sites for substrate binding and catalysis were also evaluated by site-directed mutagenesis study and activity analysis. The unique features of the MtbArgA structure will provide useful insights for inhibitor design and anti-tuberculosis drug discovery.
-Crystal structure of l-glutamate N-acetyltransferase ArgA from Mycobacterium tuberculosis.,Yang X, Wu L, Ran Y, Xu A, Zhang B, Yang X, Zhang R, Rao Z, Li J Biochim Biophys Acta. 2017 Sep 21. pii: S1570-9639(17)30225-X. doi:, 10.1016/j.bbapap.2017.09.009. PMID:28943401<ref>PMID:28943401</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5yge" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Amino-acid N-acetyltransferase]]
+[[Category: Large Structures]]
-[[Category: Myctu]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
-[[Category: Li, J]]
+[[Category: Li J]]
-[[Category: Ran, Y]]
+[[Category: Ran Y]]
-[[Category: Rao, Z]]
+[[Category: Rao Z]]
-[[Category: Wu, L]]
+[[Category: Wu L]]
-[[Category: Xu, A]]
+[[Category: Xu A]]
-[[Category: Yang, X]]
+[[Category: Yang X]]
-[[Category: Zhang, B]]
+[[Category: Zhang B]]
-[[Category: Zhang, R]]
+[[Category: Zhang R]]
-[[Category: Acetyl coenzyme some]]
-[[Category: Acetyltransferase]]
-[[Category: Arginine biosynthesis]]
-[[Category: Glutamate]]
-[[Category: Transferase]]