PDBsum entry: 2c1g

Hydrolase

PDB id: 2c1g

Contents

Protein chain

384 a.a. *

Ligands

ACT

PEG

Metals

_ZN ×3

Waters ×177

* Residue conservation analysis

PDB id:

2c1g

Name:

Hydrolase

Title:

Structure of streptococcus pneumoniae peptidoglycan deacetylase (sppgda)

Structure:

Peptidoglycan glcnac deacetylase. Chain: a. Fragment: residues 38-463. Synonym: sppgda-wt. Engineered: yes

Source:

Streptococcus pneumoniae. Organism_taxid: 171101. Strain: r6. Atcc: baa-255. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21 de3plyss.

Resolution:

1.75Å R-factor: 0.211 R-free: 0.242

Authors:

D.E.Blair,A.W.Schuttelkopf,J.I.Macrae,D.M.F.Van Aalten

Key ref:

D.E.Blair et al. (2005). Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor. Proc Natl Acad Sci U S A, 102, 15429-15434. PubMed id: 16221761 DOI: 10.1073/pnas.0504339102

Date:

14-Sep-05 Release date: 15-Sep-05

Protein chain

Q8DP63  (Q8DP63_STRR6) -  Peptidoglycan GlcNAc deacetylase

Seq: 463 a.a.

Struc: 384 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: carbohydrate metabolic process (1 term)
• Biochemical function: catalytic activity (3 terms)

DOI no: 10.1073/pnas.0504339102

Proc Natl Acad Sci U S A 102:15429-15434 (2005)

PubMed id: 16221761

Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor.

D.E.Blair, A.W.Schüttelkopf, J.I.MacRae, D.M.van Aalten.

ABSTRACT

Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA) protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. Deletion of the pgda gene has been shown to result in hypersensitivity to lysozyme and reduction of infectivity in a mouse model. SpPgdA is a member of the family 4 carbohydrate esterases, for which little structural information exists, and no catalytic mechanism has yet been defined. Here we describe the native crystal structure and product complexes of SpPgdA biochemical characterization and mutagenesis. The structural data show that SpPgdA is an elongated three-domain protein in the crystal. The structure, in combination with mutagenesis, shows that SpPgdA is a metalloenzyme using a His-His-Asp zinc-binding triad with a nearby aspartic acid and histidine acting as the catalytic base and acid, respectively, somewhat similar to other zinc deacetylases such as LpxC. The enzyme is able to accept GlcNAc(3) as a substrate (K(m) = 3.8 mM, k(cat) = 0.55 s(-1)), with the N-acetyl of the middle sugar being removed by the enzyme. The data described here show that SpPgdA and the other family 4 carbohydrate esterases are metalloenzymes and present a step toward identification of mechanism-based inhibitors for this important class of enzymes.

Selected figure(s)

Figure 2.
Fig. 2. Details of the SpPgdA active site. Close-up of the active sites of: the native SpPgdA structure in complex with the acetate product and PEG200 (SpPGDA_Ac), the SpPgdA D275N mutant in complex with sulfate and Mes (SpPGDA_SO4), and the previously determined complex of B. subtilis PdaA in complex with GlcNAc and a glycerol molecule (PDAA_GlcNAc). The five CE-4 sequence motifs (MT1-5) are shown in yellow. Side chains lining the active site cleft are shown as sticks. Residues conserved in all CE-4 esterases are magenta. Water molecules (spheres) and ligands (green sticks) are also shown. Unbiased F[o] - F[c], [calc] maps are shown at 2.25 (Mes in SpPGDA_SO4) and 12 (Zn in SpPGDA_Ac/SO4). Hydrogen bonds are shown as dashed lines in black and zinc-ligand interactions, as green dashed lines.

Figure 4.
Fig. 4. Docked GlcNAc[3] complex and reaction mechanism. (A) Sp-PgdA is shown as a ribbon, with conserved side chains. The acetate molecule as observed in the SpPgdA-acetate complex (Fig. 2) is shown as yellow sticks. GlcNAc[3] is shown as green sticks with subsites labeled in blue. Hydrogen bonds are shown as dashed lines in black, and zinc-ligand interactions are shown as magenta dashed lines. (B) As A, but viewed from the top. (C) Proposed catalytic mechanism.

Figures were selected by an automated process.