Jaime L. Stark and Kelly A. Mercier contributed equally to this work.
Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis†
Article first published online: 8 NOV 2010
Copyright © 2010 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 78, Issue 16, pages 3328–3340, December 2010
How to Cite
Stark, J. L., Mercier, K. A., Mueller, G. A., Acton, T. B., Xiao, R., Montelione, G. T. and Powers, R. (2010), Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. Proteins, 78: 3328–3340. doi: 10.1002/prot.22840
The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Allergy and Infectious Diseases.
- Issue published online: 8 NOV 2010
- Article first published online: 8 NOV 2010
- Manuscript Accepted: 11 JUL 2010
- Manuscript Revised: 7 JUL 2010
- Manuscript Received: 12 MAR 2010
- Protein Structure Initiative of the National Institutes of Health. Grant Number: U54 GM074958
- National Institute of Allergy and Infectious Diseases Nebraska. Grant Number: R21AI081154
- NIH. Grant Number: RR015468-01
- Battelle (U.S. Department of Energy Office of Biological and Environmental Research). Grant Number: KP130103
- Tobacco Settlement Biomedical Research Development Fund
- NIH (Intramural Research Program)
- National Institute of Environmental Health Sciences
- NMR structure;
- YndB Bacillus subtilis;
- NMR ligand affinity screen;
- in silico screen;
- stress response;
- symbiotic relationship
The solution structure of the Bacillus subtilis protein YndB has been solved using NMR to investigate proposed biological functions. The YndB structure exhibits the helix-grip fold, which consists of a β-sheet with two small and one long α-helix, forming a hydrophobic cavity that preferentially binds lipid-like molecules. Sequence and structure comparisons with proteins from eukaryotes, prokaryotes, and archaea suggest that YndB is very similar to the eukaryote protein Aha1, which binds to the middle domain of Hsp90 and induces ATPase activity. On the basis of these similarities, YndB has been classified as a member of the activator of Hsp90 ATPase homolog 1-like protein (AHSA1) family with a function that appears to be related to stress response. An in silico screen of a compound library of ∼18,500 lipids was used to identify classes of lipids that preferentially bind YndB. The in silico screen identified, in order of affinity, the chalcone/hydroxychalcone, flavanone, and flavone/flavonol classes of lipids, which was further verified by 2D 1H-15N HSQC NMR titration experiments with trans-chalcone, flavanone, flavone, and flavonol. All of these compounds are typically found in plants as precursors to various flavonoid antibiotics and signaling molecules. The sum of the data suggests an involvement of YndB with the stress response of B. subtilis to chalcone-like flavonoids released by plants due to a pathogen infection. The observed binding of chalcone-like molecules by YndB is likely related to thesymbiotic relationship between B. subtilis and plants. Proteins 2010. © 2010 Wiley-Liss, Inc.