6pa4: Difference between revisions
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==E. coli L-asparaginase II double mutant (T89V,K162T) in complex with L-Asp at pH 7.0== | ==E. coli L-asparaginase II double mutant (T89V,K162T) in complex with L-Asp at pH 7.0== | ||
<StructureSection load='6pa4' size='340' side='right'caption='[[6pa4]]' scene=''> | <StructureSection load='6pa4' size='340' side='right'caption='[[6pa4]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PA4 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PA4 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6pa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pa4 OCA], [https://pdbe.org/6pa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pa4 RCSB], [https://www.ebi.ac.uk/pdbsum/6pa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pa4 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6pa4" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Asparaginase 3D structures|Asparaginase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||