Solution Structure of the PAS Domain of a Thermophilic YybT Protein Homolog Reveals a Potential Ligand-binding Site

• Published in: The Journal of biological chemistry Vol. 288; no. 17; pp. 11949 - 11959
• Main Authors: Tan, Edward, Rao, Feng, Pasunooti, Swathi, Pham, Thi Huong, Soehano, Ishin, Turner, Mark S., Liew, Chong Wai, Lescar, Julien, Pervushin, Konstantin, Liang, Zhao-Xun
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 26-04-2013; American Society for Biochemistry and Molecular Biology
• Subjects: Antibiotic Resistance; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bacterial Signal Transduction; Cell Wall; Cyclic Di-AMP; Cyclic Nucleotides; Dinucleoside Phosphates - chemistry; Dinucleoside Phosphates - genetics; Dinucleoside Phosphates - metabolism; GdpP; Geobacillus - chemistry; Geobacillus - genetics; Geobacillus - metabolism; Heme; Nuclear Magnetic Resonance, Biomolecular; PAS Domain; Protein Folding; Protein Multimerization; Protein Structure and Folding; Protein Structure, Quaternary; Protein Structure, Secondary; Protein Structure, Tertiary; YybT; Cell Wall; Cyclic Di-AMP; Bacterial Signal Transduction; Heme; PAS Domain; YybT; Antibiotic Resistance; GdpP; Cyclic Nucleotides
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M112.437764

The Bacillus subtilis protein YybT (or GdpP) and its homologs were recently established as stress signaling proteins that exert their biological effect by degrading the bacterial messenger cyclic di-AMP. YybT homologs contain a small Per-ARNT-Sim (PAS) domain (∼80 amino acids) that can bind b-type heme with 1:1 stoichiometry despite the small size of the domain and the lack of a conserved heme iron-coordinating residue. We determined the solution structure of the PAS domain of GtYybT from Geobacillus thermodenitrificans by NMR spectroscopy to further probe its function. The solution structure confirms that PASGtYybT adopts the characteristic PAS fold composed of a five-stranded antiparallel β sheet and a few short α-helices. One α-helix and three central β-strands of PASGtYybT are noticeably shorter than those of the typical PAS domains. Despite the small size of the protein domain, a hydrophobic pocket is formed by the side chains of nonpolar residues stemming from the β-strands and α-helices. A set of residues in the vicinity of the pocket and in the C-terminal region at the dimeric interface exhibits perturbed NMR parameters in the presence of heme or zinc protoporphyrin. Together, the results unveil a compact PAS domain with a potential ligand-binding pocket and reinforce the view that the PASYybT domains function as regulatory domains in the modulation of cellular cyclic di-AMP concentration.
Background: c-di-AMP-degrading YybT homologs contain a PAS domain with heme binding capability.
Results: The solution structure of the PAS domain was determined to reveal a potential ligand-binding site.
Conclusion: PASYybT domains function as ligand-binding regulatory domains.
Significance: Cellular cyclic di-AMP levels are likely to be regulated by a small-molecule ligand.