Peptidoglycan-N-acetylglucosamine deacetylase Bc1960

 

Peptidoglycan N-acetylglucosamine (GlcNAc) deacetylase Bc1960 is a Bacillus cereus enzyme with backbone modifications is the Cα hydroxylation of a proline in the active site. Bc1960 is a polysaccharide deacetylase (PDA) that catalyzes the reaction of turning peptidoglycan-N-acetyl-D-glucosamine to peptidoglycan-D-glucosamine. Modification of peptidoglycan by N-deacetylation is an important factor in virulence of Helicobacter pylori, Listeria monocytogenes and Streptococcus suis.

 

Reference Protein and Structure

Sequence
Q81EK9 UniProt (3.5.1.104) IPR011330 (Sequence Homologues) (PDB Homologues)
Biological species
Bacillus cereus ATCC 14579 (Bacteria) Uniprot
PDB
4l1g - Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase from Bacillus cereus (2.336 Å) PDBe PDBsum 4l1g
Catalytic CATH Domains
3.20.20.370 CATHdb (see all for 4l1g)
Cofactors
Zinc(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:3.5.1.104)

Peptidoglycan(N-acetyl-D-glucosamine)
CHEBI:X00691X00691
+
water
CHEBI:15377ChEBI
→
Peptidoglycan-D-glucosamine
CHEBI:X00690X00690
+
acetic acid
CHEBI:15366ChEBI
Alternative enzyme names: HP310, PgdA, SpPgdA, BC1960, Peptidoglycan deacetylase, N-acetylglucosamine deacetylase, Peptidoglycan GlcNAc deacetylase, Peptidoglycan N-acetylglucosamine deacetylase, PG N-deacetylase,

Enzyme Mechanism

Introduction

In this reaction Asp80 firstly deprotonates a water molecule coordinated to the Zn2+ ion which is coordinated to the active site by His131, His135 and Asp81. This creates a hydroxide which is stabilised by Hyp171 through a bridging water molecule. The hydroxide is a strong nucleophile and as such attacks the carbonyl carbon of the substrate. A tetrahedral intermediate is formed and stabilised by the carbonyl oxygen coordinating Zn2+. The overall substrate is further stabilised by the hydoxyl group of Hyp171. His225 then proceeds to protonate the substrates nitrogen bound to the attacked carbonyl carbon releasing the acetate leaving group.

Catalytic Residues Roles

UniProt PDB* (4l1g)
His139, His143, Asp89 His131C, His135C, Asp81C Asp81, His131, His135 coordinate the Zn2+ cation. metal ligand
His233 His225C His225 protonates the nitrogen bound to the leaving group which collapses the intermediate and releases acetate from the substrate. proton donor
Asp88 Asp80C Asp80 deprotonates the water molecule coordinated to the Zn2+, turning it into a hydroxide which reacts with the substrate. proton acceptor
Pro179 X171C Hyp171 stabilises the reaction with its side chain hydroxide. It donates a hydrogen bond to the carbonyl oxygen from the substrate. It also accepts a hydrogen bond from a water molecule which interacts with the hydroxide bound to the active site Zn2+. This creates a hydrogen bond network stabilising the overall reaction. hydrogen bond acceptor, hydrogen bond donor, electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, coordination to a metal ion, bimolecular nucleophilic addition, intermediate formation, overall reactant used, intermediate collapse, overall product formed, unimolecular elimination by the conjugate base

References

  1. Prejanò M et al. (2019), Phys Chem Chem Phys, 21, 23338-23345. Why hydroxy-proline improves the catalytic power of the peptidoglycan N-deacetylase enzyme: insight from theory. DOI:10.1039/c9cp03804c. PMID:31617504.
  2. Fadouloglou VE et al. (2017), J Am Chem Soc, 139, 5330-5337. Unusual α-Carbon Hydroxylation of Proline Promotes Active-Site Maturation. DOI:10.1021/jacs.6b12209. PMID:28333455.
  3. Boneca IG (2005), Curr Opin Microbiol, 8, 46-53. The role of peptidoglycan in pathogenesis. DOI:https://doi.org/10.1016/j.mib.2004.12.008.

Step 1. The first step is the deprotonation of Asp80 of the catalytic water. This creates a nucleophile hydroxide coordinated to a Zn2+ ion.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
X171C hydrogen bond donor, hydrogen bond acceptor, electrostatic stabiliser
Asp81C metal ligand
His135C metal ligand
His131C metal ligand
Asp80C proton acceptor

Chemical Components

proton transfer

Step 2. The hydroxide coordinated by the active site and Zn2+ cation performs nucleophilic attack on the carbonyl carbon of the substrate. This is stabilised by the carbonyl oxygen coordinating to the Zn2+.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His131C metal ligand
His135C metal ligand
Asp81C metal ligand
X171C electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor

Chemical Components

coordination to a metal ion, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used

Step 3. The His225 protonates the nitrogen atom of the substrate releasing the acetate leaving group.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
X171C hydrogen bond donor, hydrogen bond acceptor, electrostatic stabiliser
Asp81C metal ligand
His135C metal ligand
His131C metal ligand
His225C proton donor

Chemical Components

intermediate collapse, overall product formed, proton transfer, ingold: unimolecular elimination by the conjugate base
Download: Image, Marvin File

Step 1. The first step is the deprotonation of Asp80 of the catalytic water. This creates a nucleophile hydroxide coordinated to a Zn2+ ion.

Step 2. The hydroxide coordinated by the active site and Zn2+ cation performs nucleophilic attack on the carbonyl carbon of the substrate. This is stabilised by the carbonyl oxygen coordinating to the Zn2+.

Step 3. The His225 protonates the nitrogen atom of the substrate releasing the acetate leaving group.

Products.

Contributors

Marko Babić, Antonio Ribeiro