View source for 5yrt


==Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal==
<StructureSection load='5yrt' size='340' side='right'caption='[[5yrt]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5yrt]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_oxytoca Klebsiella oxytoca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YRT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YRT 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]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=5yrt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yrt OCA], [https://pdbe.org/5yrt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yrt RCSB], [https://www.ebi.ac.uk/pdbsum/5yrt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yrt ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q59470_KLEOX Q59470_KLEOX] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structures of the B12 -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species.

Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12 Catalysis.,Shibata N, Sueyoshi Y, Higuchi Y, Toraya T Angew Chem Int Ed Engl. 2018 Jun 25;57(26):7830-7835. doi:, 10.1002/anie.201803591. Epub 2018 May 25. PMID:29797764<ref>PMID:29797764</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5yrt" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Klebsiella oxytoca]]
[[Category: Large Structures]]
[[Category: Shibata N]]