2M1C

HADDOCK structure of GtYybT PAS Homodimer

Summary for 2M1C

• Entry DOI: 10.2210/pdb2m1c/pdb
• NMR Information: BMRB: 18856
• Descriptor: DHH subfamily 1 protein (1 entity in total)
• Functional Keywords: pas domain, yybt, ligand binding, hydrolase
• Biological source: Geobacillus thermodenitrificans
• Total number of polymer chains: 2
• Total formula weight: 26418.66

Authors

Liang, Z.X.,Pervushin, K.,Tan, E.,Rao, F.,Pasunooti, S.,Soehano, I.,Lescar, J. (deposition date: 2012-11-25, release date: 2013-03-27, Last modification date: 2024-05-15)

Primary citation

Tan, E.,Rao, F.,Pasunooti, S.,Pham, T.H.,Soehano, I.,Turner, M.S.,Liew, C.W.,Lescar, J.,Pervushin, K.,Liang, Z.X.
Solution Structure of the PAS Domain of a Thermophilic YybT Protein Homolog Reveals a Potential Ligand-binding Site.
J.Biol.Chem., 288:11949-11959, 2013

PubMed Abstract: 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.

PubMed: 23504327
DOI: 10.1074/jbc.M112.437764

Experimental method

SOLUTION NMR