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https://hdl.handle.net/2440/70867
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Type: | Journal article |
Title: | Structural analysis of the essential resuscitation promoting factor YeaZ suggests a mechanism of nucleotide regulation through dimer reorganization |
Author: | Aydin, I. Saijo-Hamano, Y. Namba, K. Thomas, C. Roujeinikova, A. |
Citation: | PLoS One, 2011; 6(8):e23245-1-e23245-8 |
Publisher: | Public Library of Science |
Issue Date: | 2011 |
ISSN: | 1932-6203 1932-6203 |
Editor: | van Veen, H.W. |
Statement of Responsibility: | Inci Aydin, Yumiko Saijo-Hamano, Keiichi Namba, Connor Thomas and Anna Roujeinikova |
Abstract: | Background: The yeaZ gene product forms part of the conserved network YjeE/YeaZ/YgjD essential for the survival of many Gram-negative eubacteria. Among other as yet unidentified roles, YeaZ functions as a resuscitation promoting factor required for survival and resuscitation of cells in a viable but non-culturable (VBNC) state. Methodology/Principal Findings: In order to investigate in detail the structure/function relationship of this family of proteins we have performed X-ray crystallographic studies of Vibrio parahaemolyticus YeaZ. The YeaZ structure showed that it has a classic actin-like nucleotide-binding fold. Comparisons of this crystal structure to that of available homologues from E. coli, T. maritima and S. typhimurium revealed two distinctly different modes of dimer formation. In one form, prevalent in the absence of nucleotide, the putative nucleotide-binding site is incomplete, lacking a binding pocket for a nucleotide base. In the second form, residues from the second subunit complete the nucleotide-binding site. This suggests that the two dimer architectures observed in the crystal structures correspond to a free and a nucleotide-bound form of YeaZ. A multiple sequence alignment of YeaZ proteins from different bacteria allowed us to identify a large conserved hydrophobic patch on the protein surface that becomes exposed upon nucleotide-driven dimer re-arrangement. We hypothesize that the transition between two dimer architectures represents the transition between the ‘on’ and ‘off’ states of YeaZ. The effect of this transition is to alternately expose and bury a docking site for the partner protein YgjD. Conclusions/Significance: This paper provides the first structural insight into the putative mechanism of nucleotide regulation of YeaZ through dimer reorganization. Our analysis suggests that nucleotide binding to YeaZ may act as a regulator or switch that changes YeaZ shape, allowing it to switch partners between YjeE and YgjD. |
Keywords: | Vibrio parahaemolyticus Nucleotides Bacterial Proteins Blotting, Western Crystallography, X-Ray Electrophoresis, Polyacrylamide Gel Binding Sites Amino Acid Sequence Protein Conformation Protein Structure, Tertiary Protein Binding Sequence Homology, Amino Acid Models, Molecular Molecular Sequence Data Protein Multimerization |
Description: | Extent: 8p. |
Rights: | Copyright: © 2011 Aydin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
DOI: | 10.1371/journal.pone.0023245 |
Grant ID: | http://purl.org/au-research/grants/arc/DP1094619 http://purl.org/au-research/grants/arc/DP1094619 |
Published version: | http://dx.doi.org/10.1371/journal.pone.0023245 |
Appears in Collections: | Aurora harvest Molecular and Biomedical Science publications |
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File | Description | Size | Format | |
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hdl_70867.pdf | Published version | 1.99 MB | Adobe PDF | View/Open |
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