This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
4zqw
From Proteopedia
(Difference between revisions)
m (Protected "4zqw" [edit=sysop:move=sysop]) |
|||
| (5 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==CdiI from Escherichia coli EC869 in complex with a macrocyclic peptide== | |
| + | <StructureSection load='4zqw' size='340' side='right'caption='[[4zqw]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4zqw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7_str._EC869 Escherichia coli O157:H7 str. EC869]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZQW 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]] 2.001Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</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=4zqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zqw OCA], [https://pdbe.org/4zqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zqw RCSB], [https://www.ebi.ac.uk/pdbsum/4zqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zqw ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/CDII4_ECO5C CDII4_ECO5C] Immunity protein component of a toxin-immunity protein module, which functions as a cellular contact-dependent growth inhibition (CDI) system. CDI modules allow bacteria to communicate with and inhibit the growth of closely related neighboring bacteria in a contact-dependent fashion. Neutralizes the toxic activity of cognate toxin CdiA (C-terminal 289 residue CT fragment). Does not inhibit toxic activity of CdiA from other toxin-immunity modules or strains of E.coli.<ref>PMID:21829394</ref> Expression of this locus confers protection against other bacteria carrying the locus.<ref>PMID:21829394</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition mediated by the CdiB/CdiA family of two-partner secretion proteins. CdiA effectors carry diverse C-terminal toxin domains (CdiA-CT), which are delivered into neighboring target cells to inhibit growth. CDI(+) bacteria also produce CdiI immunity proteins that bind specifically to cognate CdiA-CT toxins and protect the cell from auto-inhibition. Here, we compare the structures of homologous CdiA-CT/CdiI complexes from Escherichia coli EC869 and Yersinia pseudotuberculosis YPIII to explore the evolution of CDI toxin/immunity protein interactions. Both complexes share an unusual beta-augmentation interaction, in which the toxin domain extends a beta-hairpin into the immunity protein to complete a six-stranded anti-parallel sheet. However, the specific contacts differ substantially between the two complexes. The EC869 beta-hairpin interacts mainly through direct H-bond and ion-pair interactions, whereas the YPIII beta-hairpin pocket contains more hydrophobic contacts and a network of bridging water molecules. In accord with these differences, we find that each CdiI protein only protects target bacteria from its cognate CdiA-CT toxin. The compact beta-hairpin binding pocket within the immunity protein represents a tractable system for the rationale design of small molecules to block CdiA-CT/CdiI complex formation. We synthesized a macrocyclic peptide mimic of the beta-hairpin from EC869 toxin and solved its structure in complex with cognate immunity protein. These latter studies suggest that small molecules could potentially be used to disrupt CDI toxin/immunity complexes. | ||
| - | + | Diversification of beta-Augmentation Interactions between CDI Toxin/Immunity Proteins.,Morse RP, Willett JL, Johnson PM, Zheng J, Credali A, Iniguez A, Nowick JS, Hayes CS, Goulding CW J Mol Biol. 2015 Nov 20;427(23):3766-84. doi: 10.1016/j.jmb.2015.09.020. Epub, 2015 Oct 9. PMID:26449640<ref>PMID:26449640</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 4zqw" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Escherichia coli]] | ||
| + | [[Category: Escherichia coli O157:H7 str. EC869]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Goulding CW]] | ||
| + | [[Category: Morse RP]] | ||
Current revision
CdiI from Escherichia coli EC869 in complex with a macrocyclic peptide
| |||||||||||
