Beta-lactamase (Class C)
This protein is a class C serine beta-lactamase with a substrate specificity for cephalosporins.
Reference Protein and Structure
- Sequence
-
P05364
(3.5.2.6)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Enterobacter cloacae (Bacteria)
- PDB
-
1xx2
- Refinement of P99 beta-lactamase from Enterobacter cloacae
(1.88 Å)
- Catalytic CATH Domains
-
3.40.710.10
(see all for 1xx2)
Enzyme Reaction (EC:3.5.2.6)
+
→
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
Tyr150 deprotonates the alcohol of Ser64, which initiates a nucleophilic addition to the carbonyl group of the beta-lactam ring. The tetrahedral intermediate collapses, cleaving the C-N bond, which deprotonates Tyr150. Tyr150 deprotonates water, which attacks the carbonyl carbon of the covalently attached intermediate in a nucleophilic addition. The tetrahedral intermediate collapses, eliminating Ser64, which reprotonates from Tyr150, producing the product.
Catalytic Residues Roles
| UniProt | PDB* (1xx2) | ||
| Ser84 (main-N), Ser338 (main-N) | Ser64A (main-N), Ser318A (main-N) | Forms the oxyanion hole. | hydrogen bond donor, electrostatic stabiliser |
| Ser84 | Ser64A | Acts as the catalytic nucleophile. | covalently attached, nucleofuge, nucleophile, proton acceptor, proton donor |
| Lys335, Glu292, Lys87 | Lys315A, Glu272A, Lys67A | Activates and stabilises Tyr150. | hydrogen bond donor, electrostatic stabiliser, increase acidity |
| Tyr170 | Tyr150A | Acts as the general acid/base that activates Ser64. | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
*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, bimolecular nucleophilic addition, intermediate formation, enzyme-substrate complex formation, overall reactant used, unimolecular elimination by the conjugate base, decyclisation, enzyme-substrate complex cleavage, intermediate collapse, intermediate terminated, overall product formed, native state of enzyme regeneratedReferences
- Lamotte-Brasseur J et al. (2000), Proteins, 40, 23-28. pKa calculations for class C ?-lactamases: The role of tyr-150. DOI:10.1002/(sici)1097-0134(20000701)40:1<23::aid-prot40>3.0.co;2-7. PMID:10813827.
- Awasthi S et al. (2018), J Phys Chem B, 122, 4299-4308. Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study. DOI:10.1021/acs.jpcb.8b01287. PMID:29553742.
- Oefner C et al. (1990), Nature, 343, 284-288. Refined crystal structure of β-lactamase from Citrobacter freundiiindicates a mechanism for β-lactam hydrolysis. DOI:10.1038/343284a0. PMID:2300174.
Step 1. Tyr150 deprotonates the alcohol of Ser64, which initiates a nucleophilic addition to the carbonyl group of the betalactam ring.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Ser64A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Tyr150A | hydrogen bond acceptor |
| Ser318A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Lys67A | hydrogen bond donor, electrostatic stabiliser |
| Lys315A | hydrogen bond donor, electrostatic stabiliser |
| Glu272A | hydrogen bond acceptor, electrostatic stabiliser |
| Ser64A | nucleophile |
| Tyr150A | proton acceptor |
| Ser64A | proton donor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, enzyme-substrate complex formation, overall reactant used
Step 2. The tetrahedral intermediate collapses, cleaving the C-N bond, which deprotonates Tyr150.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Ser64A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Tyr150A | hydrogen bond donor |
| Ser318A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Lys67A | hydrogen bond donor, electrostatic stabiliser, increase acidity |
| Lys315A | hydrogen bond donor, electrostatic stabiliser, increase acidity |
| Glu272A | hydrogen bond acceptor, electrostatic stabiliser |
| Ser64A | covalently attached |
| Tyr150A | proton donor |
Chemical Components
proton transfer, ingold: unimolecular elimination by the conjugate base, intermediate formation, decyclisation
Step 3. Tyr150 deprotonates water, which attacks the carbonyl carbon of the covalently attached intermediate in a nucleophilic addition.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Ser64A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Tyr150A | hydrogen bond acceptor |
| Ser318A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Lys67A | hydrogen bond donor, electrostatic stabiliser |
| Lys315A | hydrogen bond donor, electrostatic stabiliser |
| Glu272A | hydrogen bond acceptor, electrostatic stabiliser |
| Ser64A | covalently attached |
| Tyr150A | proton acceptor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used
Step 4. The tetrahedral intermediate collapses, eliminating Ser64, which reprotonates from Tyr150, producing the product.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Ser64A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Tyr150A | hydrogen bond donor |
| Ser318A (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Lys67A | hydrogen bond donor, electrostatic stabiliser, increase acidity |
| Lys315A | hydrogen bond donor, electrostatic stabiliser, increase acidity |
| Glu272A | hydrogen bond acceptor, electrostatic stabiliser |
| Tyr150A | proton donor |
| Ser64A | proton acceptor, nucleofuge |
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