Featured Article - August 2014
Short description: A first-in-family structure of a Pseudomonas-specific protein provides clues to its role in quorum sensing.
Pseudomonas aeruginosa is a pervasive environmental pathogen and leading cause of nosocomial infection, especially in immunocompromised individuals. P. aeruginosa controls expression of its virulence factors using quorum sensing (QS), the process by which small secreted signaling molecules facilitate monitoring of bacterial cell density. Components of QS systems and the virulence factors they regulate are potential targets for antimicrobial agents, but many are likely hidden among the numerous P. aeruginosa proteins that have not been functionally or structurally characterized.
Das and colleagues (PSI JCSG) have now determined the crystal structure of PA3611 (PDB 3NPD), a ∼14-kDa protein thought to be upregulated in QS, based on its secretion by wild type P. aeruginosa PAO1 but not by attenuated, QS-defective mutant strains. This is the first structural representative of the PF13652 (DUF4146) protein family, a group of Pseudomonas-specific single-domain proteins of unknown function. The crystal structure shows a twisted antiparallel β-sheet flanked by α-helices. Residue conservation analysis using CONSURF revealed a cluster of highly conserved surface residues on one side of the protein, most of which line a prominent groove.
Although sequence analysis of PA3611 using Position-Specific Iterated-BLAST failed to identify any non-Pseudomonas homologs, a search for similar structures using the FATCAT flexible alignment mode identified the C-terminal domain of Escherichia coli Era GTPase, a prokaryotic type KH domain (KH-domain type II) involved in protein and RNA binding. Comparison of the PA3611 and Era KH structures shows that, despite considerable differences in helix positions, surface residues along a helix-turn-helix motif have similar side chain chemistry. Thus, both structures share a basic region that is thought to mediate RNA binding in the Era KH domain.
Although further analysis is needed to determine the binding partners and exact role of PA3611, genomic computational analysis by the authors predicted that PA3611 is a virulence factor, with potential functional or physical interaction with PotD (PA3610), a substrate-binding protein in the polyamine uptake system implicated in QS.
D. Das et al. Crystal structure of a putative quorum sensing-regulated protein (PA3611) from the Pseudomonas-specific DUF4146 family.
Proteins. 82, 1086-92 (2014). doi:10.1002/prot.24455