1KDL image
Deposition Date 2001-11-13
Release Date 2002-08-21
Last Version Date 2024-05-01
Entry Detail
PDB ID:
1KDL
Title:
Solution structure of the amphipathic domain of YopD from Yersinia
Biological Source:
Source Organism:
(Taxon ID: )
Method Details:
Experimental Method:
Conformers Calculated:
150
Conformers Submitted:
1
Selection Criteria:
structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:YOPD protein
Gene (Uniprot):sctB
Chain IDs:A
Chain Length:23
Number of Molecules:1
Biological Source:
Ligand Molecules
Primary Citation
Conformational analysis by CD and NMR spectroscopy of a peptide encompassing the amphipathic domain of YopD from Yersinia.
Eur.J.Biochem. 269 3659 3668 (2002)
PMID: 12153562 DOI: 10.1046/j.1432-1033.2002.03051.x

Abstact

To establish an infection, Yersinia pseudotuberculosis utilizes a plasmid-encoded type III secretion machine that permits the translocation of several anti-host factors into the cytosol of target eukaryotic cells. Secreted YopD is essential for this process. Pre-secretory stabilization of YopD is mediated by an interaction with its cognate chaperone, LcrH. YopD possesses LcrH binding domains located in the N-terminus and in a predicted amphipathic domain located near the C-terminus. This latter domain is also critical for Yersinia virulence. In this study, we designed synthetic peptides encompassing the C-terminal amphipathic domain of YopD. A solution structure of YopD278-300, a peptide that strongly interacted with LcrH, was obtained by NMR methods. The structure is composed of a well-defined amphipathic alpha helix ranging from Phe280 to Tyr291, followed by a type I beta turn between residues Val292 and His295. The C-terminal truncated peptides, YopD278-292 and YopD271-292, lacked helical structure, implicating the beta turn in helix stability. An interaction between YopD278-300 and its cognate chaperone, LcrH, was observed by NMR through line-broadening effects and chemical shift differences between the free peptide and the peptide-LcrH complex. These effects were not observed for the unstructured peptide, YopD278-292, which confirms that the alpha helical structure of the YopD amphipathic domain is a critical binding region of LcrH.

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