4zqw

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(Difference between revisions)

Revision as of 06:52, 27 March 2019

CdiI from Escherichia coli EC869 in complex with a macrocyclic peptide

Structural highlights

4zqw is a 4 chain structure with sequence from Eco5c. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	cdiI4, cdiIo11, ECH7EC869_5884 (ECO5C)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] Expression of this locus confers protection against other bacteria carrying the locus.^[2]

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Poole SJ, Diner EJ, Aoki SK, Braaten BA, t'Kint de Roodenbeke C, Low DA, Hayes CS. Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems. PLoS Genet. 2011 Aug;7(8):e1002217. doi: 10.1371/journal.pgen.1002217. Epub 2011 , Aug 4. PMID:21829394 doi:http://dx.doi.org/10.1371/journal.pgen.1002217
↑ Poole SJ, Diner EJ, Aoki SK, Braaten BA, t'Kint de Roodenbeke C, Low DA, Hayes CS. Identification of functional toxin/immunity genes linked to contact-dependent growth inhibition (CDI) and rearrangement hotspot (Rhs) systems. PLoS Genet. 2011 Aug;7(8):e1002217. doi: 10.1371/journal.pgen.1002217. Epub 2011 , Aug 4. PMID:21829394 doi:http://dx.doi.org/10.1371/journal.pgen.1002217
↑ Morse RP, Willett JL, Johnson PM, Zheng J, Credali A, Iniguez A, Nowick JS, Hayes CS, Goulding CW. Diversification of beta-Augmentation Interactions between CDI Toxin/Immunity Proteins. J Mol Biol. 2015 Nov 20;427(23):3766-84. doi: 10.1016/j.jmb.2015.09.020. Epub, 2015 Oct 9. PMID:26449640 doi:http://dx.doi.org/10.1016/j.jmb.2015.09.020

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4zqw"

@@ Line 1: / Line 1: @@
 ==CdiI from Escherichia coli EC869 in complex with a macrocyclic peptide==
-<StructureSection load='4zqw' size='340' side='right' caption='[[4zqw]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='4zqw' size='340' side='right'caption='[[4zqw]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zqw]] is a 4 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZQW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zqw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco5c Eco5c]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZQW FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cdiI4, cdiIo11, ECH7EC869_5884 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=478008 ECO5C])</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4zqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zqw OCA], [http://pdbe.org/4zqw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zqw RCSB], [http://www.ebi.ac.uk/pdbsum/4zqw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zqw ProSAT]</span></td></tr>
 </table>
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Eco5c]]
+[[Category: Large Structures]]
 [[Category: Goulding, C W]]
 [[Category: Morse, R P]]

4zqw

From Proteopedia

Revision as of 06:52, 27 March 2019

CdiI from Escherichia coli EC869 in complex with a macrocyclic peptide

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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