| Title : Definition of an alpha\/beta-hydrolase fold subfamily comprising Pseudomonas quinolone signal cleaving dioxygenases - Wullich_2020_Appl.Environ.Microbiol__ |
| Author(s) : Wullich SC , Arranz San Martin A , Fetzner S |
| Ref : Applied Environmental Microbiology , : , 2020 |
| Abstract : The quinolone ring is a common core structure of natural products exhibiting antimicrobial, cytotoxic, and signaling activities. A prominent example is the Pseudomonas quinolone signal (PQS), a quorum sensing signal molecule involved in the regulation of virulence of P. aeruginosa The key reaction to quinolone inactivation and biodegradation is the cleavage of the 3-hydroxy-4(1H)-quinolone ring, catalyzed by dioxygenases (HQDs) which are members of the alpha/beta-hydrolase fold superfamily. The alpha/beta-hydrolase fold core domain consists of a beta-sheet surrounded by alpha-helices, with an active site usually containing a catalytic triad comprising a nucleophilic residue, an acidic residue, and a histidine. The nucleophile is located at the tip of a sharp turn called the "nucleophilic elbow". In this work, we developed a search workflow for the identification of HQD proteins from databases. Search and validation criteria include a [H-x(2)-W] motif at the nucleophilic elbow, a [HFP-x(4)-P] motif comprising the catalytic histidine, the presence of a helical cap domain, the positioning of the triad's acidic residue at the end of beta-strand 6, and a set of conserved hydrophobic residues contributing to the substrate cavity. The 161 candidate proteins identified from the UniProtKB database originate from environmental and plant-associated microorganisms from all domains of life. Verification and characterization of HQD activity of 9 new candidate proteins confirmed the reliability of the search strategy, and suggested residues correlating with distinct substrate preferences. Among the new HQDs, PQS dioxygenases from Nocardia farcinica, N. cyriacigeorgica, and Streptomyces bingchenggensis likely are part of a catabolic pathway for alkylquinolone utilization.ImportanceFunctional annotation of protein sequences is a major requirement for the investigation of metabolic pathways and the identification of sought-after biocatalysts. To identify heterocyclic ring-cleaving dioxygenases within the huge superfamily of alpha/beta-hydrolase fold proteins, we defined search and validation criteria for the primarily motif-based identification of 3-hydroxy-4(1H)-quinolone 2,4-dioxygenases (HQD). HQDs are key enzymes for the inactivation of metabolites which can have signaling, antimicrobial, or cytotoxic functions. The HQD candidates detected in this study occur particularly in environmental and plant-associated microorganisms. Because HQDs active towards the Pseudomonas quinolone signal (PQS) likely contribute to interactions within microbial communities and modulate the virulence of Pseudomonas aeruginosa, we analyzed the catalytic properties of a PQS-cleaving subset of HQDs, and specified characteristics to identify PQS-cleaving dioxygenases within the HQD family. |
| ESTHER : Wullich_2020_Appl.Environ.Microbiol__ |
| PubMedSearch : Wullich_2020_Appl.Environ.Microbiol__ |
| PubMedID: 32086305 |
Wullich SC, Arranz San Martin A, Fetzner S (2020)
Definition of an alpha\/beta-hydrolase fold subfamily comprising Pseudomonas quinolone signal cleaving dioxygenases
Applied Environmental Microbiology
:
Wullich SC, Arranz San Martin A, Fetzner S (2020)
Applied Environmental Microbiology
: