Beta-lactamase (Class B1)

 

Beta-lactamase is a key enzyme in antibiotic resistance, catalysing the cleavage of the essential beta-lactam ring structure in penicillin and cephalosporinase type antibiotics. Substrate specificity varies considerably within the beta-lactamases, with some enzymes preferring penicillins and some cephalosporins.

 

Reference Protein and Structure

Sequence
P04190 UniProt (3.5.2.6) IPR001279 (Sequence Homologues) (PDB Homologues)
Biological species
Bacillus cereus (Bacteria) Uniprot
PDB
1bc2 - ZN-DEPENDENT METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS (1.9 Å) PDBe PDBsum 1bc2
Catalytic CATH Domains
3.60.15.10 CATHdb (see all for 1bc2)
Cofactors
Zinc(2+) (1) 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

This entry describes the monometallic mechanism where the zinc ion is bound in the His3 site. Here the zinc activated water initiates the reaction, Asp90 deprotonates the OH of the tetrahedral intermediate and finally, the intermediate collapses, with the nitrogen group re-protonating from Asp90. The active site starting state is regenerated from bulk solvent, the zinc activates the water to re-form the initiating hydroxide ion (not shown).

Catalytic Residues Roles

UniProt PDB* (1bc2)
Asp120 Asp90A Acts as a general acid/base, abstracting a proton from the added water molecule. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Asn210 Asn180A Helps stabilise the negatively charged intermediates. hydrogen bond donor, electrostatic stabiliser
His116, His179, His118 His86A, His149A, His88A Binds the Zn(II) 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 addition, overall reactant used, intermediate formation, proton transfer, unimolecular elimination by the conjugate base

References

  1. Garau G et al. (2005), J Mol Biol, 345, 785-795. A Metallo-β-lactamase Enzyme in Action: Crystal Structures of the Monozinc Carbapenemase CphA and its Complex with Biapenem. DOI:10.1016/j.jmb.2004.10.070. PMID:15588826.
  2. Page MI et al. (2008), Bioinorg Chem Appl, 2008, 1-14. The Mechanisms of Catalysis by Metallo -Lactamases. DOI:10.1155/2008/576297. PMID:18551183.
  3. Wang Z et al. (1999), Curr Opin Chem Biol, 3, 614-622. Metallo-β-lactamase: structure and mechanism. DOI:10.1016/s1367-5931(99)00017-4. PMID:10508665.
  4. Carfi A et al. (1998), Acta Crystallogr D Biol Crystallogr, 54, 313-323. 1.85 Å Resolution Structure of the ZincII β-Lactamase from Bacillus cereus . DOI:10.1107/s0907444997010627.
  5. BOUNAGA S et al. (1998), Biochem J, 331, 703-711. The mechanism of catalysis and the inhibition of the Bacillus cereus zinc-dependent β-lactamase. DOI:10.1042/bj3310703.

Step 1. The Zinc-activated water initiates a nucleophilic attack on the carbonyl carbon of the beta-lactam ring in an addition reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp90A hydrogen bond acceptor
Asn180A hydrogen bond donor, electrostatic stabiliser
His88A metal ligand
His149A metal ligand
His86A metal ligand

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation

Step 2. Asp90 deprotonates the hydroxyl group of the added water.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp90A hydrogen bond acceptor
Asn180A hydrogen bond donor, electrostatic stabiliser
His88A metal ligand
His149A metal ligand
His86A metal ligand
Asp90A proton acceptor

Chemical Components

proton transfer, intermediate formation

Step 3. The oxyanion formed from the initial attack performs an elimination reaction, breaking the C-N bond, the nitrogen of which deprotonates the Asp90.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp90A hydrogen bond donor
Asn180A hydrogen bond donor, electrostatic stabiliser
His88A metal ligand
His149A metal ligand
His86A metal ligand
Asp90A proton donor

Chemical Components

proton transfer, ingold: unimolecular elimination by the conjugate base, intermediate formation
Download: Image, Marvin File

Step 1. The Zinc-activated water initiates a nucleophilic attack on the carbonyl carbon of the beta-lactam ring in an addition reaction.

Step 2. Asp90 deprotonates the hydroxyl group of the added water.

Step 3. The oxyanion formed from the initial attack performs an elimination reaction, breaking the C-N bond, the nitrogen of which deprotonates the Asp90.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Sophie T. Williams, Katherine Ferris