6nx8: Difference between revisions
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<StructureSection load='6nx8' size='340' side='right'caption='[[6nx8]], [[Resolution|resolution]] 1.85Å' scene=''> | <StructureSection load='6nx8' size='340' side='right'caption='[[6nx8]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6nx8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NX8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NX8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6nx8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NX8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NX8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6nx6|6nx6]], [[6nx7|6nx7]], [[6nx9|6nx9]], [[6nxa|6nxa]], [[6nxb|6nxb]], [[6nxc|6nxc]], [[6nxd|6nxd]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6nx6|6nx6]], [[6nx7|6nx7]], [[6nx9|6nx9]], [[6nxa|6nxa]], [[6nxb|6nxb]], [[6nxc|6nxc]], [[6nxd|6nxd]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ansB, b2957, JW2924 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </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=6nx8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nx8 OCA], [http://pdbe.org/6nx8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nx8 RCSB], [http://www.ebi.ac.uk/pdbsum/6nx8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nx8 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=6nx8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nx8 OCA], [http://pdbe.org/6nx8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nx8 RCSB], [http://www.ebi.ac.uk/pdbsum/6nx8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nx8 ProSAT]</span></td></tr> | ||
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<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
Active sites of enzymes are highly optimized for interactions with specific substrates, thus binding of opportunistic ligands is usually observed only in the absence of native substrates or products. However, during growth of crystals required for structure determination enzymes are often exposed to conditions significantly divergent from the native ones, leading to binding of unexpected ligands to active sites even in the presence of substrates. Failing to recognize this possibility may lead to incorrect interpretation of experimental results and to faulty conclusions. Here, we present several examples of binding of a citrate anion to the active sites of E. coli L-asparaginases I and II, even in the presence of the native substrate, L-Asn. A part of this report focuses on a comprehensive re-interpretation of structural results published previously for complexes of type I L-asparaginase (EcAI) from E. coli. In two re-refined structures a citrate anion forms an acyl-enzyme reaction intermediate with the catalytic threonine. These results emphasize the importance of careful and critical analysis during interpretation of crystallographic data. | |||
Opportunistic complexes of E. coli L-asparaginases with citrate anions.,Lubkowski J, Chan W, Wlodawer A Sci Rep. 2019 Jul 30;9(1):11070. doi: 10.1038/s41598-019-46432-0. PMID:31363102<ref>PMID:31363102</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Asparaginase]] | [[Category: Asparaginase]] | ||
[[Category: Ecoli]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Lubkowski, J]] | [[Category: Lubkowski, J]] | ||
Revision as of 20:39, 20 November 2019
ECAII(T89V,K162T) MUTANT IN COMPLEX WITH CITRATE AT PH 6.2ECAII(T89V,K162T) MUTANT IN COMPLEX WITH CITRATE AT PH 6.2
Structural highlights
Publication Abstract from PubMedActive sites of enzymes are highly optimized for interactions with specific substrates, thus binding of opportunistic ligands is usually observed only in the absence of native substrates or products. However, during growth of crystals required for structure determination enzymes are often exposed to conditions significantly divergent from the native ones, leading to binding of unexpected ligands to active sites even in the presence of substrates. Failing to recognize this possibility may lead to incorrect interpretation of experimental results and to faulty conclusions. Here, we present several examples of binding of a citrate anion to the active sites of E. coli L-asparaginases I and II, even in the presence of the native substrate, L-Asn. A part of this report focuses on a comprehensive re-interpretation of structural results published previously for complexes of type I L-asparaginase (EcAI) from E. coli. In two re-refined structures a citrate anion forms an acyl-enzyme reaction intermediate with the catalytic threonine. These results emphasize the importance of careful and critical analysis during interpretation of crystallographic data. Opportunistic complexes of E. coli L-asparaginases with citrate anions.,Lubkowski J, Chan W, Wlodawer A Sci Rep. 2019 Jul 30;9(1):11070. doi: 10.1038/s41598-019-46432-0. PMID:31363102[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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