4P7O: Structure of Escherichia coli PgaB C-terminal domain, P1 crystal form

Citation:
Abstract
Poly-beta-1,6-N-acetyl-D-glucosamine (PNAG) is an exopolysaccharide produced by a wide variety of medically important bacteria. Polyglucosamine subunit B (PgaB) is responsible for the de-N-acetylation of PNAG, a process required for polymer export and biofilm formation. PgaB is located in the periplasm and likely bridges the inner membrane synthesis and outer membrane export machinery. Here, we present structural, functional, and molecular simulation data that suggest PgaB associates with PNAG continuously during periplasmic transport. We show that the association of PgaB's N- and C-terminal domains forms a cleft required for the binding and de-N-acetylation of PNAG. Molecular dynamics (MD) simulations of PgaB show a binding preference for N-acetylglucosamine (GlcNAc) to the N-terminal domain and glucosammonium to the C-terminal domain. Continuous ligand binding density is observed that extends around PgaB from the N-terminal domain active site to an electronegative groove on the C-terminal domain that would allow for a processive mechanism. PgaB's C-terminal domain (PgaB310-672) directly binds PNAG oligomers with dissociation constants of approximately 1-3 mM, and the structures of PgaB310-672 in complex with beta-1,6-(GlcNAc)6, GlcNAc, and glucosamine reveal a unique binding mode suitable for interaction with de-N-acetylated PNAG (dPNAG). Furthermore, PgaB310-672 contains a beta-hairpin loop (betaHL) important for binding PNAG that was disordered in previous PgaB42-655 structures and is highly dynamic in the MD simulations. We propose that conformational changes in PgaB310-672 mediated by the betaHL on binding of PNAG/dPNAG play an important role in the targeting of the polymer for export and its release.
PDB ID: 4P7ODownload
MMDB ID: 121188
PDB Deposition Date: 2014/3/27
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 1.48  Å
Source Organism:
Similar Structures:
Biological Unit for 4P7O: monomeric; determined by author
Molecular Components in 4P7O
Label Count Molecule
Protein (1 molecule)
1
Poly-beta-1,6-n-acetyl-d-glucosamine N-deacetylase(Gene symbol: pgaB)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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