4F9D

Structure of Escherichia coli PgaB 42-655 in complex with nickel

Summary for 4F9D

• Entry DOI: 10.2210/pdb4f9d/pdb
• Related: 4F9J
• Descriptor: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase, NICKEL (II) ION, ACETIC ACID, ... (6 entities in total)
• Functional Keywords: family 4 carbohydrate esterase, tim barrel, hydrolase, deacetylase, carbohydrate/sugar binding
• Biological source: Escherichia coli
• Cellular location: Cell outer membrane; Lipid-anchor; Periplasmic side (Probable): P75906
• Total number of polymer chains: 2
• Total formula weight: 143148.29

Authors

Little, D.J.,Poloczek, J.,Whitney, J.C.,Robinson, H.,Nitz, M.,Howell, P.L. (deposition date: 2012-05-18, release date: 2012-07-25, Last modification date: 2024-02-28)

Primary citation

Little, D.J.,Poloczek, J.,Whitney, J.C.,Robinson, H.,Nitz, M.,Howell, P.L.
The Structure and Metal Dependent Activity of Escherichia coli PgaB Provides Insight into the Partial De-N-acetylation of Poly-b-1,6-N-acetyl-D-glucosamine
J.Biol.Chem., 287:31126-31137, 2012

PubMed Abstract: Exopolysaccharides are required for the development and integrity of biofilms produced by a wide variety of bacteria. In Escherichia coli, partial de-N-acetylation of the exopolysaccharide poly-β-1,6-N-acetyl-D-glucosamine (PNAG) by the periplasmic protein PgaB is required for polysaccharide intercellular adhesin-dependent biofilm formation. To understand the molecular basis for PNAG de-N-acetylation, the structure of PgaB in complex with Ni(2+) and Fe(3+) have been determined to 1.9 and 2.1 Å resolution, respectively, and its activity on β-1,6-GlcNAc oligomers has been characterized. The structure of PgaB reveals two (β/α)(x) barrel domains: a metal-binding de-N-acetylase that is a member of the family 4 carbohydrate esterases (CE4s) and a domain structurally similar to glycoside hydrolases. PgaB displays de-N-acetylase activity on β-1,6-GlcNAc oligomers but not on the β-1,4-(GlcNAc)(4) oligomer chitotetraose and is the first CE4 member to exhibit this substrate specificity. De-N-acetylation occurs in a length-dependent manor, and specificity is observed for the position of de-N-acetylation. A key aspartic acid involved in de-N-acetylation, normally seen in other CE4s, is missing in PgaB, suggesting that the activity of PgaB is attenuated to maintain the low levels of de-N-acetylation of PNAG observed in vivo. The metal dependence of PgaB is different from most CE4s, because PgaB shows increased rates of de-N-acetylation with Co(2+) and Ni(2+) under aerobic conditions, and Co(2+), Ni(2+) and Fe(2+) under anaerobic conditions, but decreased activity with Zn(2+). The work presented herein will guide inhibitor design to combat biofilm formation by E. coli and potentially a wide range of medically relevant bacteria producing polysaccharide intercellular adhesin-dependent biofilms.

PubMed: 22810235
DOI: 10.1074/jbc.M112.390005

Experimental method

X-RAY DIFFRACTION (1.9 Å)