2M1C

HADDOCK structure of GtYybT PAS Homodimer

2M1C の概要

• エントリーDOI: 10.2210/pdb2m1c/pdb
• NMR情報: BMRB: 18856
• 分子名称: DHH subfamily 1 protein (1 entity in total)
• 機能のキーワード: pas domain, yybt, ligand binding, hydrolase
• 由来する生物種: Geobacillus thermodenitrificans
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 26418.66

構造登録者

Liang, Z.X.,Pervushin, K.,Tan, E.,Rao, F.,Pasunooti, S.,Soehano, I.,Lescar, J. (登録日: 2012-11-25, 公開日: 2013-03-27, 最終更新日: 2024-05-15)

主引用文献

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

実験手法

SOLUTION NMR