PDBsum entry: 1dd6

Hydrolase

PDB id: 1dd6

Contents

Protein chains

216 a.a. *

Ligands

SO4

MCI ×2

Metals

_ZN ×4

Waters ×340

* Residue conservation analysis

PDB id:

1dd6

Name:

Hydrolase

Title:

Imp-1 metallo beta-lactamase from pseudomonas aeruginosa in complex with a mercaptocarboxylate inhibitor

Structure:

Imp-1 metallo beta-lactamase. Chain: a, b. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.198 R-free: 0.259

Authors:

N.O.Concha,C.A.Janson,P.Rowling,S.Pearson,C.A.Cheever, B.P.Clarke,C.Lewis,M.Galleni,J.M.Frere,D.J.Payne, J.H.Bateson,S.S.Abdel-Meguid

Key ref:

N.O.Concha et al. (2000). Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor. Biochemistry, 39, 4288-4298. PubMed id: 10757977 DOI: 10.1021/bi992569m

Date:

08-Nov-99 Release date: 08-Nov-00

Protein chains

P52699  (BLAB_SERMA) -  Beta-lactamase IMP-1

Seq: 246 a.a.

Struc: 216 a.a.

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: Zinc

 Gene Ontology (GO) functional annotation 

• Biological process: response to antibiotic (2 terms)
• Biochemical function: hydrolase activity (4 terms)

DOI no: 10.1021/bi992569m

Biochemistry 39:4288-4298 (2000)

PubMed id: 10757977

Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor.

N.O.Concha, C.A.Janson, P.Rowling, S.Pearson, C.A.Cheever, B.P.Clarke, C.Lewis, M.Galleni, J.M.Frère, D.J.Payne, J.H.Bateson, S.S.Abdel-Meguid.

ABSTRACT

Metallo beta-lactamase enzymes confer antibiotic resistance to bacteria by catalyzing the hydrolysis of beta-lactam antibiotics. This relatively new form of resistance is spreading unchallenged as there is a current lack of potent and selective inhibitors of metallo beta-lactamases. Reported here are the crystal structures of the native IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor, 2-[5-(1-tetrazolylmethyl)thien-3-yl]-N-[2-(mercaptomethyl)-4 -(phenylb utyrylglycine)]. The structures were determined by molecular replacement, and refined to 3.1 A (native) and 2.0 A (complex) resolution. Binding of the inhibitor in the active site induces a conformational change that results in closing of the flap and transforms the active site groove into a tunnel-shaped cavity enclosing 83% of the solvent accessible surface area of the inhibitor. The inhibitor binds in the active site through interactions with residues that are conserved among metallo beta-lactamases; the inhibitor's carboxylate group interacts with Lys161, and the main chain amide nitrogen of Asn167. In the "oxyanion hole", the amide carbonyl oxygen of the inhibitor interacts through a water molecule with the side chain of Asn167, the inhibitor's thiolate bridges the two Zn(II) ions in the active site displacing the bridging water, and the phenylbutyryl side chain binds in a hydrophobic pocket (S1) at the base of the flap. The flap is displaced 2.9 A compared to the unbound structure, allowing Trp28 to interact edge-to-face with the inhibitor's thiophene ring. The similarities between this inhibitor and the beta-lactam substrates suggest a mode of substrate binding and the role of the conserved residues in the active site. It appears that the metallo beta-lactamases bind their substrates by establishing a subset of binding interactions near the catalytic center with conserved characteristic chemical groups of the beta-lactam substrates. These interactions are complemented by additional nonspecific binding between the more variable groups in the substrates and the flexible flap. This unique mode of binding of the mercaptocarboxylate inhibitor in the enzyme active site provides a binding model for metallo beta-lactamase inhibition with utility for future drug design.