8bk3: Difference between revisions

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'''Unreleased structure'''


The entry 8bk3 is ON HOLD  until Paper Publication
==Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with diepoxide ketone 1==
<StructureSection load='8bk3' size='340' side='right'caption='[[8bk3]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8bk3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BK3 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]] 2.15&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=QXU:1-[(2~{S},3~{R})-3-phenyloxiran-2-yl]ethanone'>QXU</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=8bk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8bk3 OCA], [https://pdbe.org/8bk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8bk3 RCSB], [https://www.ebi.ac.uk/pdbsum/8bk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8bk3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LDT2_MYCTO LDT2_MYCTO] Generates 3->3 cross-links in peptidoglycan, catalyzing the cleavage of the mDap(3)-D-Ala(4) bond of a tetrapeptide donor stem and the formation of a bond between the carbonyl of mDap(3) of the donor stem and the side chain of mDap(3) of the acceptor stem. Is specific for donor substrates containing a stem tetrapeptide since it cannot use pentapeptide stems. Is essential for virulence in a mouse model of acute infection.<ref>PMID:20305661</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Epoxides are an established class of electrophilic alkylating agents that react with nucleophilic protein residues. We report alphabeta,alpha'beta'-diepoxyketones (DEKs) as a new type of mechanism-based inhibitors of nucleophilic cysteine enzymes. Studies with the L,D-transpeptidase Ldt(Mt2) from Mycobacterium tuberculosis and the main protease from SARS-CoV-2 (M(pro)) reveal that following epoxide ring opening by a nucleophilic cysteine, further reactions can occur, leading to irreversible alkylation.


Authors:  
alphabeta,alpha'beta'-Diepoxyketones are mechanism-based inhibitors of nucleophilic cysteine enzymes.,de Munnik M, Lithgow J, Brewitz L, Christensen KE, Bates RH, Rodriguez-Miquel B, Schofield CJ Chem Commun (Camb). 2023 Oct 26;59(86):12859-12862. doi: 10.1039/d3cc02932h. PMID:37815791<ref>PMID:37815791</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 8bk3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Schofield CJ]]
[[Category: De Munnik M]]
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