7mdf: Difference between revisions

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 <table><tr><td colspan='2'>[[7mdf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_CFT073 Escherichia coli CFT073]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MDF 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]] 2.3&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=97N:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-HEXADEC-9-ENOATE'>97N</scene>, <scene name='pdbligand=AV0:2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl+4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside'>AV0</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z9A:methyl+N~2~-[4-(4-bromophenyl)butanoyl]-D-asparaginyl-L-alaninate'>Z9A</scene>, <scene name='pdbligand=Z9G:N~2~-[4-(4-bromophenyl)butanoyl]-D-asparagine'>Z9G</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=97N:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-HEXADEC-9-ENOATE'>97N</scene>, <scene name='pdbligand=AV0:2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl+4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside'>AV0</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z9A:methyl+N~2~-[4-(4-bromophenyl)butanoyl]-D-asparaginyl-L-alaninate'>Z9A</scene>, <scene name='pdbligand=Z9G:(2~{R})-4-azanyl-2-[4-(4-bromophenyl)butanoylamino]-4-oxidanylidene-butanoic+acid'>Z9G</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=7mdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mdf OCA], [https://pdbe.org/7mdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mdf RCSB], [https://www.ebi.ac.uk/pdbsum/7mdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mdf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/Q0P7K6_ECOLX Q0P7K6_ECOLX] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.[ARBA:ARBA00003808]
+[https://www.uniprot.org/uniprot/A0A0H2V8D3_ECOL6 A0A0H2V8D3_ECOL6]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Colibactin, a DNA cross-linking agent produced by gut bacteria, is implicated in colorectal cancer. Its biosynthesis uses a prodrug resistance mechanism: a non-toxic precursor assembled in the cytoplasm is activated after export to the periplasm. This activation is mediated by ClbP, an inner-membrane peptidase with an N-terminal periplasmic catalytic domain and a C-terminal three-helix transmembrane domain. Although the transmembrane domain is required for colibactin activation, its role in catalysis is unclear. Our structure of full-length ClbP bound to a product analog reveals an interdomain interface important for substrate binding and enzyme stability and interactions that explain the selectivity of ClbP for the N-acyl-D-asparagine prodrug motif. Based on structural and biochemical evidence, we propose that ClbP dimerizes to form an extended substrate-binding site that can accommodate a pseudodimeric precolibactin with its two terminal prodrug motifs in the two ClbP active sites, thus enabling the coordinated activation of both electrophilic warheads.
+Structural basis of colibactin activation by the ClbP peptidase.,Velilla JA, Volpe MR, Kenney GE, Walsh RM Jr, Balskus EP, Gaudet R Nat Chem Biol. 2023 Feb;19(2):151-158. doi: 10.1038/s41589-022-01142-z. Epub 2022 , Oct 17. PMID:36253550<ref>PMID:36253550</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7mdf" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>