PDBsum entry 4ev4

Hydrolase/antibiotic

PDB id: 4ev4

Contents

Protein chain

270 a.a.

Ligands

MER

EDO ×4

Waters ×437

PDB id:

4ev4

Name:

Hydrolase/antibiotic

Title:

Crystal structure of serratia fonticola carbapenemase sfc-1 e166a mutant with the acylenzyme intermediate of meropenem

Structure:

Carbapenem-hydrolizing beta-lactamase sfc-1. Chain: a. Fragment: unp residues 27-309. Engineered: yes. Mutation: yes

Source:

Serratia fonticola. Organism_taxid: 47917. Strain: utad54. Gene: blasfc-1, sfc-1. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.30Å R-factor: 0.116 R-free: 0.155

Authors:

F.Fonseca,J.Spencer

Key ref:

F.Fonseca et al. (2012). The basis for carbapenem hydrolysis by class A β-lactamases: a combined investigation using crystallography and simulations. J Am Chem Soc, 134, 18275-18285. PubMed id: 23030300

Date:

25-Apr-12 Release date: 23-May-12

Protein chain

Q6JP75  (Q6JP75_SERFO) -  beta-lactamase from Serratia fonticola

Seq: 309 a.a.

Struc: 270 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.2.6 - beta-lactamase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a beta-lactam + H2O = a substituted beta-amino acid
• Cofactor: Zn(2+)

J Am Chem Soc 134:18275-18285 (2012)

PubMed id: 23030300

The basis for carbapenem hydrolysis by class A β-lactamases: a combined investigation using crystallography and simulations.

F.Fonseca, E.I.Chudyk, M.W.van der Kamp, A.Correia, A.J.Mulholland, J.Spencer.

ABSTRACT

Carbapenems are the most potent β-lactam antibiotics and key drugs for treating infections by Gram-negative bacteria. In such organisms, β-lactam resistance arises principally from β-lactamase production. Although carbapenems escape the activity of most β-lactamases, due in the class A enzymes to slow deacylation of the covalent acylenzyme intermediate, carbapenem-hydrolyzing class A β-lactamases are now disseminating in clinically relevant bacteria. The reasons why carbapenems are substrates for these enzymes, but inhibit other class A β-lactamases, remain to be fully established. Here, we present crystal structures of the class A carbapenemase SFC-1 from Serratia fonticola and of complexes of its Ser70 Ala (Michaelis) and Glu166 Ala (acylenzyme) mutants with the carbapenem meropenem. These are the first crystal structures of carbapenem complexes of a class A carbapenemase. Our data reveal that, in the SFC-1 acylenzyme complex, the meropenem 6α-1R-hydroxyethyl group interacts with Asn132, but not with the deacylating water molecule. Molecular dynamics simulations indicate that this mode of binding occurs in both the Michaelis and acylenzyme complexes of wild-type SFC-1. In carbapenem-inhibited class A β-lactamases, it is proposed that the deacylating water molecule is deactivated by interaction with the carbapenem 6α-1R-hydroxyethyl substituent. Structural comparisons with such enzymes suggest that in SFC-1 subtle repositioning of key residues (Ser70, Ser130, Asn132 and Asn170) enlarges the active site, permitting rotation of the carbapenem 6α-1R-hydroxyethyl group and abolishing this contact. Our data show that SFC-1, and by implication other such carbapenem-hydrolyzing enzymes, uses Asn132 to orient bound carbapenems for efficient deacylation and prevent their interaction with the deacylating water molecule.