3a18: Difference between revisions

Revision as of 14:06, 1 November 2023

Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (soaked crystal)

Structural highlights

3a18 is a 4 chain structure with sequence from Rhodococcus erythropolis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	BXO, HEM
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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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OCA

[1] 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

[2] 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

[3] 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

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='3a18' size='340' side='right'caption='[[3a18]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3a18]] 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=3A18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A18 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3a18]] 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=3A18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A18 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BXO:(1Z)-BUTANAL+OXIME'>BXO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.8&#8491;</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]], [[3a16|3a16]], [[3a17|3a17]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BXO:(1Z)-BUTANAL+OXIME'>BXO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=3a18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a18 OCA], [https://pdbe.org/3a18 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a18 RCSB], [https://www.ebi.ac.uk/pdbsum/3a18 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a18 ProSAT]</span></td></tr>
 </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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Mycobacterium erythropolis gray and thornton 1928]]
-[[Category: Aliphatic aldoxime dehydratase]]
 [[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]]

3a18: Difference between revisions

Revision as of 14:06, 1 November 2023

Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (soaked crystal)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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