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| | <StructureSection load='3a16' size='340' side='right'caption='[[3a16]], [[Resolution|resolution]] 1.60Å' scene=''> | | <StructureSection load='3a16' size='340' side='right'caption='[[3a16]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a16]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A16 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a16]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A16 FirstGlance]. <br> |
| - | </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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PXO:(1Z)-PROPANAL+OXIME'>PXO</scene></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]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a15|3a15]], [[3a17|3a17]], [[3a18|3a18]]</div></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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PXO:(1Z)-PROPANAL+OXIME'>PXO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">oxd ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 "Mycobacterium erythropolis" Gray and Thornton 1928])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aliphatic_aldoxime_dehydratase Aliphatic aldoxime dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.5 4.99.1.5] </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=3a16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a16 OCA], [https://pdbe.org/3a16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a16 RCSB], [https://www.ebi.ac.uk/pdbsum/3a16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a16 ProSAT]</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=3a16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a16 OCA], [https://pdbe.org/3a16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a16 RCSB], [https://www.ebi.ac.uk/pdbsum/3a16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a16 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/OXD_RHOER OXD_RHOER] Catalyzes the dehydration of aldoximes to their corresponding nitrile (PubMed:16233624, PubMed:19740758). Is active toward various arylalkyl- and alkyl-aldoximes, and to a lesser extent toward aryl-aldoximes (PubMed:16233624).<ref>PMID:16233624</ref> <ref>PMID:19740758</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Mycobacterium erythropolis gray and thornton 1928]] | |
| - | [[Category: Aliphatic aldoxime dehydratase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Aono, S]] | + | [[Category: Rhodococcus erythropolis]] |
| - | [[Category: Asano, Y]] | + | [[Category: Aono S]] |
| - | [[Category: Kato, Y]] | + | [[Category: Asano Y]] |
| - | [[Category: Sawai, H]] | + | [[Category: Kato Y]] |
| - | [[Category: Shiro, Y]] | + | [[Category: Sawai H]] |
| - | [[Category: Sugimoto, H]] | + | [[Category: Shiro Y]] |
| - | [[Category: Beta barrel]]
| + | [[Category: Sugimoto H]] |
| - | [[Category: Heme protein]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
OXD_RHOER Catalyzes the dehydration of aldoximes to their corresponding nitrile (PubMed:16233624, PubMed:19740758). Is active toward various arylalkyl- and alkyl-aldoximes, and to a lesser extent toward aryl-aldoximes (PubMed:16233624).[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Aldoxime dehydratase (Oxd) catalyzes the dehydration of aldoximes (R-CH=N-OH) to their corresponding nitrile (R-C triple bond N). Oxd is a heme-containing enzyme that catalyzes the dehydration reaction as its physiological function. We have determined the first two structures of Oxd: the substrate-free OxdRE at 1.8 A resolution and the n-butyraldoxime- and propionaldoxime-bound OxdREs at 1.8 and 1.6 A resolutions, respectively. Unlike other heme enzymes, the organic substrate is directly bound to the heme iron in OxdRE. We determined the structure of the Michaelis complex of OxdRE by using the unique substrate binding and activity regulation properties of Oxd. The Michaelis complex was prepared by x-ray cryoradiolytic reduction of the ferric dead-end complex in which Oxd contains a Fe(3+) heme form. The crystal structures reveal the mechanism of substrate recognition and the catalysis of OxdRE.
X-ray crystal structure of michaelis complex of aldoxime dehydratase.,Sawai H, Sugimoto H, Kato Y, Asano Y, Shiro Y, Aono S J Biol Chem. 2009 Nov 13;284(46):32089-96. Epub 2009 Sep 8. PMID:19740758[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kato Y, Yoshida S, Xie SX, Asano Y. Aldoxime dehydratase co-existing with nitrile hydratase and amidase in the iron-type nitrile hydratase-producer Rhodococcus sp. N-771. J Biosci Bioeng. 2004;97(4):250-9. PMID:16233624 doi:10.1016/S1389-1723(04)70200-5
- ↑ Sawai H, Sugimoto H, Kato Y, Asano Y, Shiro Y, Aono S. X-ray crystal structure of michaelis complex of aldoxime dehydratase. J Biol Chem. 2009 Nov 13;284(46):32089-96. Epub 2009 Sep 8. PMID:19740758 doi:10.1074/jbc.M109.018762
- ↑ Sawai H, Sugimoto H, Kato Y, Asano Y, Shiro Y, Aono S. X-ray crystal structure of michaelis complex of aldoxime dehydratase. J Biol Chem. 2009 Nov 13;284(46):32089-96. Epub 2009 Sep 8. PMID:19740758 doi:10.1074/jbc.M109.018762
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