9axj
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==Cystathionine gamma lyase from Thermobifida fusca in an amino crotonate form== | |
| + | <StructureSection load='9axj' size='340' side='right'caption='[[9axj]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[9axj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobifida_fusca Thermobifida fusca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9AXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9AXJ 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]] 1.5Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=9axj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9axj OCA], [https://pdbe.org/9axj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9axj RCSB], [https://www.ebi.ac.uk/pdbsum/9axj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9axj ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A9P2TCP3_THEFU A0A9P2TCP3_THEFU] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pyridoxal phosphate (PLP)-dependent enzymes play essential roles in metabolism and have found applications for organic synthesis and as enzyme therapeutics. The vinylglycine ketimine (VGK) subfamily hosts a growing set of enzymes that play diverse roles in primary and secondary metabolism. However, the molecular determinates of substrate specificity and the complex acid-base chemistry that enables VGK catalysis remain enigmatic. We use a recently discovered amino acid gamma-lyase as a model system to probe catalysis in this enzyme family. We discovered that two stereochemically distinct proton transfer pathways occur. Combined kinetic and spectroscopic analysis revealed that progression through the catalytic cycle is correlated with the presence of an H-bond donor after Cgamma of an amino acid substrate, suggesting substrate binding is kinetically coupled to a conformational change. High-resolution X-ray crystallography shows that cystathionine-gamma-lyases generate an s-trans intermediate and that this geometry is likely conserved throughout the VGK family. An H-bond acceptor in the active site templates substrate binding but does so by pre-organizing substrates away from catalytically productive orientations. Mutagenesis eliminates this pre-organization, such that there is a relaxation of the substrate specificity, but an increase in k (cat) for diverse substrates. We exploit this information to perform preparative scale alpha,beta,beta-tri-deuteration of polar amino acids. Together, these data untangle a complex mode of substrate specificity and provide a foundation for the future study and applications of VGK enzymes. | ||
| - | + | Elucidation of the stereochemical mechanism of cystathionine gamma-lyase reveals how substrate specificity constrains catalysis.,Zmich A, Perkins LJ, Bingman C, Buller AR ACS Catal. 2024 Aug 2;14(15):11196-11204. doi: 10.1021/acscatal.4c02281. Epub , 2024 Jul 11. PMID:39391268<ref>PMID:39391268</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 9axj" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Thermobifida fusca]] | ||
| + | [[Category: Bingman CA]] | ||
| + | [[Category: Buller AR]] | ||
| + | [[Category: Perkins LJ]] | ||
| + | [[Category: Zmich AP]] | ||
Current revision
Cystathionine gamma lyase from Thermobifida fusca in an amino crotonate form
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