3w08: Difference between revisions
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==Crystal structure of aldoxime dehydratase== | ==Crystal structure of aldoxime dehydratase== | ||
<StructureSection load='3w08' size='340' side='right'caption='[[3w08]]' scene=''> | <StructureSection load='3w08' size='340' side='right'caption='[[3w08]], [[Resolution|resolution]] 1.80Å' 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=3W08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W08 FirstGlance]. <br> | <table><tr><td colspan='2'>[[3w08]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_chlororaphis Pseudomonas chlororaphis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3W08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W08 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=3w08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w08 OCA], [https://pdbe.org/3w08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w08 RCSB], [https://www.ebi.ac.uk/pdbsum/3w08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w08 ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=3w08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w08 OCA], [https://pdbe.org/3w08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w08 RCSB], [https://www.ebi.ac.uk/pdbsum/3w08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w08 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/OXD_PSECL OXD_PSECL] Catalyzes the dehydration of aldoximes to their corresponding nitrile (PubMed:12773527, PubMed:23382199). Aliphatic aldoximes are more effective substrates than aromatic aldoximes (PubMed:12773527). Shows high activity with butyraldoxime and acetaldoxime, but only weak activity with the aromatic aldoxime pyridine-2-aldoxime (PubMed:12773527). Cannot use benzaldoxime, isonitrosoacetophenone and pyridine-4-aldoxime (PubMed:12773527). Is involved in the metabolism of aldoxime in vivo (PubMed:12773527).<ref>PMID:12773527</ref> <ref>PMID:23382199</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Aldoxime dehydratase (OxdA), which is a unique heme protein, catalyzes the dehydration of an aldoxime to a nitrile even in the presence of water in the reaction mixture. Unlike the utilization of H(2)O(2) or O(2) as a mediator of catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron. Here, we determined the crystal structure of OxdA. We then constructed OxdA mutants in which each of the polar amino acids lying within approximately 6 A of the iron atom of the heme was converted to alanine. Among the purified mutant OxdAs, S219A had completely lost and R178A exhibited a reduction in the activity. Together with this finding, the crystal structural analysis of OxdA and spectroscopic and electrostatic potential analyses of the wild-type and mutant OxdAs suggest that S219 plays a key role in the catalysis, forming a hydrogen bond with the substrate. Based on the spatial arrangement of the OxdA active site and the results of a series of mutagenesis experiments, we propose the detailed catalytic mechanism of general aldoxime dehydratases: (i) S219 stabilizes the hydroxy group of the substrate to increase its basicity; (ii) H320 acts as an acid-base catalyst; and (iii) R178 stabilizes the heme, and would donate a proton to and accept one from H320. | |||
Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis.,Nomura J, Hashimoto H, Ohta T, Hashimoto Y, Wada K, Naruta Y, Oinuma KI, Kobayashi M Proc Natl Acad Sci U S A. 2013 Feb 4. PMID:23382199<ref>PMID:23382199</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3w08" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Pseudomonas chlororaphis]] | |||
[[Category: Hara K]] | [[Category: Hara K]] | ||
[[Category: Hashimoto H]] | [[Category: Hashimoto H]] | ||