6AU1

Structure of the PgaB (BpsB) glycoside hydrolase domain from Bordetella bronchiseptica

Summary for 6AU1

• Entry DOI: 10.2210/pdb6au1/pdb
• Descriptor: Putative hemin storage protein, SULFATE ION, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: deacetylase, glycoside hydrolase, hydrolase, pnag, biofilm
• Biological source: Bordetella bronchiseptica
• Total number of polymer chains: 2
• Total formula weight: 82108.18

Authors

Little, D.J.,Bamford, N.C.,Howell, P.L. (deposition date: 2017-08-30, release date: 2018-04-18, Last modification date: 2023-10-04)

Primary citation

Little, D.J.,Pfoh, R.,Le Mauff, F.,Bamford, N.C.,Notte, C.,Baker, P.,Guragain, M.,Robinson, H.,Pier, G.B.,Nitz, M.,Deora, R.,Sheppard, D.C.,Howell, P.L.
PgaB orthologues contain a glycoside hydrolase domain that cleaves deacetylated poly-beta (1,6)-N-acetylglucosamine and can disrupt bacterial biofilms.
PLoS Pathog., 14:e1006998-e1006998, 2018

PubMed Abstract: Poly-β(1,6)-N-acetyl-D-glucosamine (PNAG) is a major biofilm component of many pathogenic bacteria. The production, modification, and export of PNAG in Escherichia coli and Bordetella species require the protein products encoded by the pgaABCD operon. PgaB is a two-domain periplasmic protein that contains an N-terminal deacetylase domain and a C-terminal PNAG binding domain that is critical for export. However, the exact function of the PgaB C-terminal domain remains unclear. Herein, we show that the C-terminal domains of Bordetella bronchiseptica PgaB (PgaBBb) and E. coli PgaB (PgaBEc) function as glycoside hydrolases. These enzymes hydrolyze purified deacetylated PNAG (dPNAG) from Staphylococcus aureus, disrupt PNAG-dependent biofilms formed by Bordetella pertussis, Staphylococcus carnosus, Staphylococcus epidermidis, and E. coli, and potentiate bacterial killing by gentamicin. Furthermore, we found that PgaBBb was only able to hydrolyze PNAG produced in situ by the E. coli PgaCD synthase complex when an active deacetylase domain was present. Mass spectrometry analysis of the PgaB-hydrolyzed dPNAG substrate showed a GlcN-GlcNAc-GlcNAc motif at the new reducing end of detected fragments. Our 1.76 Å structure of the C-terminal domain of PgaBBb reveals a central cavity within an elongated surface groove that appears ideally suited to recognize the GlcN-GlcNAc-GlcNAc motif. The structure, in conjunction with molecular modeling and site directed mutagenesis led to the identification of the dPNAG binding subsites and D474 as the probable catalytic acid. This work expands the role of PgaB within the PNAG biosynthesis machinery, defines a new glycoside hydrolase family GH153, and identifies PgaB as a possible therapeutic agent for treating PNAG-dependent biofilm infections.

PubMed: 29684093
DOI: 10.1371/journal.ppat.1006998

Experimental method

X-RAY DIFFRACTION (1.76 Å)