Peptidoglycan glycosyltransferase

 

Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the polymerization of peptidoglycan (lipid II) into linear glycan chains, which is an essential part of peptidoglycan biosynthesis. It uses lipid II precursors to synthesize glycan chains of the peptidoglycan, the polymeric layer in the cell wall of bacteria. PGT inhibition leads to bacterial cell wall lysis, making it an important topic of research.

 

Reference Protein and Structure

Sequence
Q99T05 UniProt (2.4.1.129) IPR022978 (Sequence Homologues) (PDB Homologues)
Biological species
Staphylococcus aureus subsp. aureus Mu50 (Bacteria) Uniprot
PDB
3vmt - Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with a Lipid II analog (2.299 Å) PDBe PDBsum 3vmt
Catalytic CATH Domains
1.10.3810.10 CATHdb (see all for 3vmt)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:2.4.1.129)

[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)]n-diphospho-ditrans,polycis-undecaprenol polyanion
CHEBI:78435ChEBI
+
lipid II(3-)
CHEBI:60033ChEBI
→
ditrans,polycis-undecaprenyl diphosphate(3-)
CHEBI:58405ChEBI
+
CHEBI:X00676X00676
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: PG-II, Bactoprenyldiphospho-N-acetylmuramoyl-(N-acetyl-D-glucosaminyl)-pentapeptide:peptidoglycan N-acetylmuramoyl-N-acetyl-D-glucosaminyltransferase, Penicillin binding protein (3 or 1B), Peptidoglycan transglycosylase, Peptidoglycan TGase, Undecaprenyldiphospho-(N-acetyl-D-glucosaminyl-(1->4)-N-acetyl-D-muramoylpentapeptide):undecaprenyldiphospho-(N-acetyl-D-glucosaminyl-(1->4)-N-acetyl-D-muramoylpentapeptide) disaccharidetransferase,

Enzyme Mechanism

Introduction

Peptidoglycan glycosyltransferases polymerize the glycan chain or lipid II chain of the bacterial peptidoglycan. A magnesium ion in the enzyme's active site stabilizes the diphosphate of the lipid II donor molecule, while the catalytic residues Ser132, Gln136, and Gly131 act as metal ligands for the magnesium ion. This polymerization is an SN2 nucleophilic reaction catalysed by Glu100.

Catalytic Residues Roles

UniProt PDB* (3vmt)
Glu100 Glu100(94)A Base catalyst, assists the SN2 nucleophilic attack that forms lipid II linkage. activator
Ser132, Gln136, Gly131 (main-C) Ser132(126)A, Gln136(130)A, Gly131(125)A (main-C) Binding motif for the magnesium ion in the active site. metal ligand
*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

bimolecular nucleophilic substitution, proton transfer, overall reactant used, overall product formed

References

  1. Goossens K et al. (2020), J Chem Inf Model, 60, 5513-5528. A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. DOI:10.1021/acs.jcim.0c00377. PMID:32786224.
  2. Punekar AS et al. (2018), Cell Surf, 2, 54-66. The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization. DOI:10.1016/j.tcsw.2018.06.002. PMID:30046666.
  3. Derouaux A et al. (2013), Front Immunol, 4, 78-. Peptidoglycan glycosyltransferase substrate mimics as templates for the design of new antibacterial drugs. DOI:10.3389/fimmu.2013.00078. PMID:23543824.

Step 1. SN2 nucleophilic attack by the polysaccharide strand at the donor site to the acceptor polysaccharide strand, assisted by Glu100 forming a lipid II linkage.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser132(126)A metal ligand
Gln136(130)A metal ligand
Gly131(125)A (main-C) metal ligand
Glu100(94)A activator

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, overall reactant used, overall product formed
Download: Image, Marvin File

Step 1. SN2 nucleophilic attack by the polysaccharide strand at the donor site to the acceptor polysaccharide strand, assisted by Glu100 forming a lipid II linkage.

Products.

Introduction

Peptidoglycan glycosyltransferases polymerise the glycan chain or lipid II chain of the bacterial peptidoglycan. Magnesium ion found in the enzyme's active site and stabilizes the diphosphate of the lipid II donor molecule, while the catalytic residues Ser132, Gln136 and Gly131 act as metal ligands for the magnesium ion. This polymerisation is a SN1 reaction and it is less favourable than the SN2 reaction, as shown by QM/MM calculations.

Catalytic Residues Roles

UniProt PDB* (3vmt)
Glu100 Glu100(94)A Base catalyst, assist the nucleophilic reaction that forms the lipid II linkage. nucleophile
Ser132, Gln136, Gly131 (main-C) Ser132(126)A, Gln136(130)A, Gly131(125)A (main-C) Biding motif for the active site Magnesium ion. metal ligand
*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

bimolecular nucleophilic substitution, overall product formed

References

  1. Lee SS et al. (2011), Nat Chem Biol, 7, 631-638. Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase. DOI:10.1038/nchembio.628. PMID:21822275.
  2. Goossens K et al. (2020), J Chem Inf Model, 60, 5513-5528. A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. DOI:10.1021/acs.jcim.0c00377. PMID:32786224.
  3. Punekar AS et al. (2018), Cell Surf, 2, 54-66. The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization. DOI:10.1016/j.tcsw.2018.06.002. PMID:30046666.
  4. Huang C et al. (2012),Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with a Lipid II analog. DOI:10.2210/pdb3vmt/pdb.

Step 1. Nucleophilic attack by Glu10, leaving group departs.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu100(94)A nucleophile
Ser132(126)A metal ligand
Gln136(130)A metal ligand
Gly131(125)A (main-C) metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution

Step 2. The departed leaving group of the donor molecule deprotonates the acceptor molecule, which in turn carries out a nucleophilic attack (SN1) on the sugar part of the donor molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser132(126)A metal ligand
Gln136(130)A metal ligand
Gly131(125)A (main-C) metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution, overall product formed
Download: Image, Marvin File

Step 1. Nucleophilic attack by Glu10, leaving group departs.

Step 2. The departed leaving group of the donor molecule deprotonates the acceptor molecule, which in turn carries out a nucleophilic attack (SN1) on the sugar part of the donor molecule.

Products.

Contributors

Yordanos Abeje, Noa Marson