6SQX

Insights into a novel NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida

Summary for 6SQX

• Entry DOI: 10.2210/pdb6sqx/pdb
• Descriptor: Peptide-binding protein, CHLORIDE ION, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: nlpc/p60, cell wall hydrolases, crystallography x-ray, d, l-endopeptidase, hydrolase
• Biological source: Photobacterium damsela subsp. piscicida (causative agent of fish pasteurellosis)
• Total number of polymer chains: 2
• Total formula weight: 117525.35

Authors

Lisboa, J.,Pereira, P.J.B.,dos Santos, N.M.S. (deposition date: 2019-09-04, release date: 2020-09-30, Last modification date: 2024-01-24)

Primary citation

Lisboa, J.,Pereira, C.,Rifflet, A.,Ayala, J.,Terceti, M.S.,Barca, A.V.,Rodrigues, I.,Pereira, P.J.B.,Osorio, C.R.,Garcia-Del Portillo, F.,Gomperts Boneca, I.,do Vale, A.,Dos Santos, N.M.S.
A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria.
Msphere, 6:-, 2021

PubMed Abstract: Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from subsp. (), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( lpC-like rotein ) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the γ-d-glutamyl--diaminopimelic acid bond. However, PnpA does not cleave the PG of or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the type II secretion system and degrades the PG of and This suggests that PnpA is used by to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG. Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that subsp. , a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.

PubMed: 33536321
DOI: 10.1128/mSphere.00736-20

Experimental method

X-RAY DIFFRACTION (1.4 Å)