7s8w: Difference between revisions
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==Amycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinylbenzoate synthase R266Q mutant in complex with N-succinylphenylglycine== | ==Amycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinylbenzoate synthase R266Q mutant in complex with N-succinylphenylglycine== | ||
<StructureSection load='7s8w' size='340' side='right'caption='[[7s8w]]' scene=''> | <StructureSection load='7s8w' size='340' side='right'caption='[[7s8w]], [[Resolution|resolution]] 2.90Å' 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=7S8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S8W FirstGlance]. <br> | <table><tr><td colspan='2'>[[7s8w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7S8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7S8W FirstGlance]. <br> | ||
</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=7s8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s8w OCA], [https://pdbe.org/7s8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s8w RCSB], [https://www.ebi.ac.uk/pdbsum/7s8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s8w ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=8JI:N-succinyl-L-phenylglycine'>8JI</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/o-succinylbenzoate_synthase o-succinylbenzoate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.113 4.2.1.113] </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=7s8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7s8w OCA], [https://pdbe.org/7s8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7s8w RCSB], [https://www.ebi.ac.uk/pdbsum/7s8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7s8w ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Catalytic promiscuity is the coincidental ability to catalyze nonbiological reactions in the same active site as the native biological reaction. Several lines of evidence show that catalytic promiscuity plays a role in the evolution of new enzyme functions. Thus, studying catalytic promiscuity can help identify structural features that predispose an enzyme to evolve new functions. This study identifies a potentially preadaptive residue in a promiscuous N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) enzyme from Amycolatopsis sp. T-1-60. This enzyme belongs to a branch of the OSBS family which includes many catalytically promiscuous NSAR/OSBS enzymes. R266 is conserved in all members of the NSAR/OSBS subfamily. However, the homologous position is usually hydrophobic in other OSBS subfamilies, whose enzymes lack NSAR activity. The second-shell amino acid R266 is close to the catalytic acid/base K263, but it does not contact the substrate, suggesting that R266 could affect the catalytic mechanism. Mutating R266 to glutamine in Amycolatopsis NSAR/OSBS profoundly reduces NSAR activity but moderately reduces OSBS activity. This is due to a 1000-fold decrease in the rate of proton exchange between the substrate and the general acid/base catalyst K263. This mutation is less deleterious for the OSBS reaction because K263 forms a cation-pi interaction with the OSBS substrate and/or the intermediate, rather than acting as a general acid/base catalyst. Together, the data explain how R266 contributes to NSAR reaction specificity and was likely an essential preadaptation for the evolution of NSAR activity. | |||
Second-Shell Amino Acid R266 Helps Determine N-Succinylamino Acid Racemase Reaction Specificity in Promiscuous N-Succinylamino Acid Racemase/o-Succinylbenzoate Synthase Enzymes.,Truong DP, Rousseau S, Machala BW, Huddleston JP, Zhu M, Hull KG, Romo D, Raushel FM, Sacchettini JC, Glasner ME Biochemistry. 2021 Nov 30. doi: 10.1021/acs.biochem.1c00627. PMID:34845903<ref>PMID:34845903</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7s8w" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Glasner | [[Category: O-succinylbenzoate synthase]] | ||
[[Category: Rousseau S]] | [[Category: Glasner, M E]] | ||
[[Category: Sacchettini | [[Category: Rousseau, S]] | ||
[[Category: Truong | [[Category: Sacchettini, J C]] | ||
[[Category: Truong, D P]] | |||
[[Category: Complex]] | |||
[[Category: Dehydratase]] | |||
[[Category: Isomerase]] | |||
[[Category: Mutant]] | |||
[[Category: Racemase]] | |||
Revision as of 17:01, 15 December 2021
Amycolatopsis sp. T-1-60 N-succinylamino acid racemase/o-succinylbenzoate synthase R266Q mutant in complex with N-succinylphenylglycine
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