2M1C | pdb_00002m1c

HADDOCK structure of GtYybT PAS Homodimer

• PDB DOI: https://doi.org/10.2210/pdb2M1C/pdb
• BMRB: 18856

• Classification: HYDROLASE
• Organism(s): Geobacillus thermodenitrificans NG80-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-25 Released: 2013-03-27 
• Deposition Author(s): Liang, Z.X., Pervushin, K., Tan, E., Rao, F., Pasunooti, S., Soehano, I., Lescar, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 4 
• Selection Criteria: Top 4 structures from HADDOCK webserver 

Literature

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

Tan, E., Rao, F., Pasunooti, S., Pham, T.H., Soehano, I., Turner, M.S., Liew, C.W., Lescar, J., Pervushin, K., Liang, Z.X.

(2013) J Biological Chem 288: 11949-11959

• PubMed: 23504327 
• DOI: https://doi.org/10.1074/jbc.M112.437764
• Primary Citation Related Structures: 
  2M1C


• 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.

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Organizational Affiliation: 
• Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.42 kDa 
• Atom Count: 1,856 
• Modeled Residue Count: 226 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DHH subfamily 1 protein	A, B	113	Geobacillus thermodenitrificans NG80-2	Mutation(s): 0  Gene Names: DHH subfamily 1, GTNG_3419 EC: 3.1.4.59
UniProt
Find proteins for A4ITV2 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4ITV2  Go to UniProtKB:  A4ITV2

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 4 
• Selection Criteria: Top 4 structures from HADDOCK webserver 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Liang, Z.X., Pervushin, K., Tan, E., Rao, F., Pasunooti, S., Soehano, I., Lescar, J.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references