Beta-lactamase (Class B1)

 

The L1 metallo-beta-lactamase from Stenotrophomonas maltophilia is unique among beta-lactamases in that it is tetrameric. S. maltophilia has emerged as a significant hospital-derived pathogen of immunocompromised hosts such as cancer, cystic fibrosis and transplant patients. L1 is localised to the periplasm and hydrolyses carbapenem drugs, conferring antibiotic resistance.

L1 is a Class B1 metallo-beta-lactamases as it binds two Zn(II) ions for the hydrolytic reaction, but its Zn2 binding site is different to most B1 type enzymes (it is also known as an L1 type 3 beta-lactamse).

 

Reference Protein and Structure

Sequence
P52700 UniProt (3.5.2.6) IPR001279 (Sequence Homologues) (PDB Homologues)
Biological species
Stenotrophomonas maltophilia (Bacteria) Uniprot
PDB
1sml - METALLO BETA LACTAMASE L1 FROM STENOTROPHOMONAS MALTOPHILIA (1.7 Å) PDBe PDBsum 1sml
Catalytic CATH Domains
3.60.15.10 CATHdb (see all for 1sml)
Cofactors
Zinc(2+) (2) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:3.5.2.6)

beta-lactam
CHEBI:35627ChEBI
+
water
CHEBI:15377ChEBI
→
substituted beta-amino acids
CHEBI:33705ChEBI
Alternative enzyme names: Beta-lactamase A, B, C, Beta-lactamase AME I, Beta-lactamase I-III, Ampicillinase, Cephalosporin-beta-lactamase, Cephalosporinase, Exopenicillinase, Neutrapen, Penicillin beta-lactamase, Penicillin amido-beta-lactamhydrolase, Penicillinase, Penicillinase I, II,

Enzyme Mechanism

Introduction

In this mechanism, the Zn1 polarises the substrate carbonyl to activate the group as an electrophile. A hydroxide ion bridges the zinc ions. This is nucleophilic and attacks the substrate carbonyl. The tetrahedral transition state is stabilised by Zn1, a helix dipole and Tyr 191. The substrate ring amide is cleaved, with the nitrogen leaving as an anion, stabilised by Zn2 acting as a superacid. The other end of the amide is a carboxylic acid. Finally, a water molecule, acidified by the zinc ions, protonates the nitroanion. The resulting hydroxide can be nucleophilic in the next catalytic cycle.

Catalytic Residues Roles

UniProt PDB* (1sml)
Tyr212 Tyr191A Part of the oxyanion hole that stabilises the negatively charged transition state. hydrogen bond donor, electrostatic stabiliser
His105, His181, His107 His84A, His160A, His86A Binds one of the catalytic zinc ions metal ligand
Asp109, His110, His246 Asp88A, His89A, His225A Binds one of the catalytic zinc ions. 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 reactant used, decyclisation, intermediate formation, proton transfer, overall product formed, intermediate terminated

References

  1. Xu D et al. (2007), J Am Chem Soc, 129, 10814-10822. Antibiotic Deactivation by a Dizinc β-Lactamase:  Mechanistic Insights from QM/MM and DFT Studies. DOI:10.1021/ja072532m. PMID:17691780.
  2. Ullah JH et al. (1998), J Mol Biol, 284, 125-136. The crystal structure of the L1 metallo-β-lactamase from Stenotrophomonas maltophilia at 1.7 å resolution. DOI:10.1006/jmbi.1998.2148. PMID:9811546.

Step 1. Zinc activated water initiates a nucleophilic attack on the carbonyl of the beta-lactam ring, forming a tetrahedral transition state that is stabilised by Tyr191, before collapsing back to break the C-N bond.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr191A hydrogen bond donor, electrostatic stabiliser
His84A metal ligand
His86A metal ligand
Asp88A metal ligand
His89A metal ligand
His160A metal ligand
His225A metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, decyclisation, intermediate formation

Step 2. The negatively charged nitrogen group deprotonates an incoming water molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His84A metal ligand
His86A metal ligand
Asp88A metal ligand
His89A metal ligand
His160A metal ligand
His225A metal ligand
Tyr191A electrostatic stabiliser

Chemical Components

proton transfer, overall reactant used, overall product formed, intermediate terminated
Download: Image, Marvin File

Step 1. Zinc activated water initiates a nucleophilic attack on the carbonyl of the beta-lactam ring, forming a tetrahedral transition state that is stabilised by Tyr191, before collapsing back to break the C-N bond.

Step 2. The negatively charged nitrogen group deprotonates an incoming water molecule.

Products.

Introduction

In this mechanism, the Zn1 polarises the substrate carbonyl to activate the group as an electrophile. A hydroxide ion bridges the zinc ions. This is nucleophilic and attacks the substrate carbonyl forming a tetrahedral intermediate that is stabilised by Zn1, a helix dipole and Tyr 191. The intermediate collapses and the substrate ring amide is cleaved, with the nitrogen leaving as an anion and reprotonating from a water molecule, acidified by the zinc ions. The resulting hydroxide can be nucleophilic in the next catalytic cycle.

Catalytic Residues Roles

UniProt PDB* (1sml)
Tyr212 Tyr191A Tyr 191 is part of the oxyanion hole, stabilising the tetrahedral transition state. This may be directly or via a water molecule. hydrogen bond donor, electrostatic stabiliser
His105, His181, His107, Asp109, His110, His246 His84A, His160A, His86A, Asp88A, His89A, His225A Binds one of the catalytic zinc ions. 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 reactant used, decyclisation, intermediate formation, proton transfer, overall product formed, intermediate terminated

References

  1. Xu D et al. (2007), J Am Chem Soc, 129, 10814-10822. Antibiotic Deactivation by a Dizinc β-Lactamase:  Mechanistic Insights from QM/MM and DFT Studies. DOI:10.1021/ja072532m. PMID:17691780.
  2. Wang Z et al. (1999), Biochemistry, 38, 10013-10023. On the Mechanism of the Metallo-β-lactamase fromBacteroides fragilis†. DOI:10.1021/bi990356r. PMID:10433708.
  3. Ullah JH et al. (1998), J Mol Biol, 284, 125-136. The crystal structure of the L1 metallo-β-lactamase from Stenotrophomonas maltophilia at 1.7 å resolution. DOI:10.1006/jmbi.1998.2148. PMID:9811546.

Step 1. Zinc activated water initiates a nucleophilic attack on the carbonyl of the beta-lactam ring, forming a tetrahedral intermediate that is stabilised by Tyr191.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr191A hydrogen bond donor, electrostatic stabiliser
His84A metal ligand
His86A metal ligand
Asp88A metal ligand
His89A metal ligand
His160A metal ligand
His225A metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, decyclisation, intermediate formation

Step 2. The tetrahedral intermediate then collapses and the nitrogen group then deprotonates an incoming water molecule.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr191A electrostatic stabiliser
His84A metal ligand
His86A metal ligand
Asp88A metal ligand
His89A metal ligand
His160A metal ligand
His225A metal ligand

Chemical Components

proton transfer, overall reactant used, overall product formed, intermediate terminated
Download: Image, Marvin File

Step 1. Zinc activated water initiates a nucleophilic attack on the carbonyl of the beta-lactam ring, forming a tetrahedral intermediate that is stabilised by Tyr191.

Step 2. The tetrahedral intermediate then collapses and the nitrogen group then deprotonates an incoming water molecule.

Products.

Contributors

Gemma L. Holliday, Jonathan T. W. Ng