8PFA

X-ray structure of the Thermus thermophilus K167R mutant of the PilF-GSPIIB domain in the c-di-GMP bound state

Summary for 8PFA

• Entry DOI: 10.2210/pdb8pfa/pdb
• Related: 8PDK
• Descriptor: c-di-GMP binding domain of the ATPase enzyme PilF, 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one), SULFATE ION, ... (5 entities in total)
• Functional Keywords: pilt class, gspii, ligand binding, c-di-gmp, motor protein
• Biological source: Thermus thermophilus HB27
• Total number of polymer chains: 2
• Total formula weight: 35231.82

Authors

Neissner, K.,Woehnert, J. (deposition date: 2023-06-15, release date: 2024-06-26, Last modification date: 2025-01-08)

Primary citation

Neissner, K.,Keller, H.,Kirchner, L.,Dusterhus, S.,Duchardt-Ferner, E.,Averhoff, B.,Wohnert, J.
The structural basis for high-affinity c-di-GMP binding to the GSPII-B domain of the traffic ATPase PilF from Thermus thermophilus.
J.Biol.Chem., 301:108041-108041, 2024

PubMed Abstract: c-di-GMP is an important second messenger in bacteria regulating, for example motility, biofilm formation, cell wall biosynthesis, infectivity, and natural transformability. It binds to a multitude of intracellular receptors. This includes proteins containing general secretory pathway II (GSPII) domains such as the N-terminal domain of the Vibrio cholerae ATPase MshE (MshEN) which binds c-di-GMP with two copies of a 24-amino acids sequence motif. The traffic ATPase PilF from Thermus thermophilus is important for type IV pilus biogenesis, twitching motility, surface attachment, and natural DNA-uptake and contains three consecutive homologous GPSII domains. We show that only two of these domains bind c-di-GMP and define the structural basis for the exceptional high affinity of the GSPII-B domain for c-di-GMP, which is 83-fold higher than that of the prototypical MshEN domain. Our work establishes an extended consensus sequence for the c-di-GMP-binding motif and highlights the role of hydrophobic residues for high-affinity recognition of c-di-GMP. Our structure is the first example for a c-di-GMP-binding domain not relying on arginine residues for ligand recognition. We also show that c-di-GMP-binding induces local unwinding of an α-helical turn as well as subdomain reorientation to reinforce intermolecular contacts between c-di-GMP and the C-terminal subdomain. Abolishing c-di-GMP binding to GSPII-B reduces twitching motility and surface attachment but not natural DNA-uptake. Overall, our work contributes to a better characterization of c-di-GMP binding in this class of effector domains, allows the prediction of high-affinity c-di-GMP-binding family members, and advances our understanding of the importance of c-di-GMP binding for T4P-related functions.

PubMed: 39615687
DOI: 10.1016/j.jbc.2024.108041

Experimental method

X-RAY DIFFRACTION (1.8 Å)