4P7L

Structure of Escherichia coli PgaB C-terminal domain, P212121 crystal form

4P7L の概要

• エントリーDOI: 10.2210/pdb4p7l/pdb
• 関連するPDBエントリー: 4F9D 4F9J 4P7N 4P7O 4P7Q 4P7R
• 分子名称: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase, 1,2-ETHANEDIOL, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: beta alpha barrel, carbohydrate binding, glycosyl hydrolase fold, hydrolase
• 由来する生物種: Escherichia coli K12
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 42539.39

構造登録者

Little, D.J.,Li, G.,Ing, C.,DiFrancesco, B.,Bamford, N.C.,Robinson, H.,Nitz, M.,Pomes, R.,Howell, P.L. (登録日: 2014-03-27, 公開日: 2014-07-02, 最終更新日: 2023-09-27)

主引用文献

Little, D.J.,Li, G.,Ing, C.,DiFrancesco, B.R.,Bamford, N.C.,Robinson, H.,Nitz, M.,Pomes, R.,Howell, P.L.
Modification and periplasmic translocation of the biofilm exopolysaccharide poly-beta-1,6-N-acetyl-D-glucosamine.
Proc.Natl.Acad.Sci.USA, 111:11013-11018, 2014

PubMed Abstract: Poly-β-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 ∼1-3 mM, and the structures of PgaB310-672 in complex with β-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 β-hairpin loop (βHL) 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 βHL on binding of PNAG/dPNAG play an important role in the targeting of the polymer for export and its release.

PubMed: 24994902
DOI: 10.1073/pnas.1406388111

実験手法

X-RAY DIFFRACTION (1.802 Å)