7mdf: Difference between revisions
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==Full-length S95A ClbP bound to N-acyl-D-asparagine analog== | |||
<StructureSection load='7mdf' size='340' side='right'caption='[[7mdf]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<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]] 2.3Å</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/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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </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> | |||
[[Category: Escherichia coli CFT073]] | |||
[[Category: Large Structures]] | |||
[[Category: Gaudet R]] | |||
[[Category: Velilla JA]] | |||
[[Category: Volpe MR]] | |||
Latest revision as of 14:34, 30 October 2024
Full-length S95A ClbP bound to N-acyl-D-asparagine analogFull-length S95A ClbP bound to N-acyl-D-asparagine analog
Structural highlights
FunctionPublication Abstract from PubMedColibactin, 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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