6paa: Difference between revisions

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-'''Unreleased structure'''
-The entry 6paa is ON HOLD
+==E. coli L-asparaginase II mutant (T12V) in complex with L-Asp at pH 5.5==
+<StructureSection load='6paa' size='340' side='right'caption='[[6paa]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6paa]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PAA FirstGlance]. <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]] 1.85&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6paa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6paa OCA], [https://pdbe.org/6paa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6paa RCSB], [https://www.ebi.ac.uk/pdbsum/6paa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6paa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ASPG2_ECOLI ASPG2_ECOLI]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Twenty crystal structures of the complexes of l-asparaginase with l-Asn, l-Asp, and succinic acid that are currently available in the Protein Data Bank, as well as 11 additional structures determined in the course of this project, were analyzed in order to establish the level of conservation of the geometric parameters describing interactions between the substrates and the active site of the enzymes. We found that such stereochemical relationships are highly conserved, regardless of the organism from which the enzyme was isolated, specific crystallization conditions, or the nature of the ligands. Analysis of the geometry of the interactions, including Burgi-Dunitz and Flippin-Lodge angles, indicated that Thr12 (Escherichia coli asparaginase II numbering) is optimally placed to be the primary nucleophile in the most likely scenario utilizing a double-displacement mechanism, whereas catalysis through a single-displacement mechanism appears to be the least likely.
-Authors:
+Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase.,Lubkowski J, Wlodawer A Protein Sci. 2019 Oct;28(10):1850-1864. doi: 10.1002/pro.3709. Epub 2019 Aug 29. PMID:31423681<ref>PMID:31423681</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6paa" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Asparaginase 3D structures|Asparaginase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Lubkowski J]]
+[[Category: Wlodawer A]]