PDBsum entry 3e2k

Hydrolase/hydrolase inhibitor

PDB id: 3e2k

Contents

Protein chains

261 a.a. *

160 a.a. *

Waters ×204

* Residue conservation analysis

PDB id:

3e2k

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of the kpc-2 beta-lactamase/beta-lactamase inhibitor protein (blip)

Structure:

Carbapenemase. Chain: a, b. Fragment: unp residues 30-293. Synonym: class a carbapenemase, beta-lactamase, class a carbapenemase kpc-2. Engineered: yes. Mutation: yes. Beta-lactamase inhibitory protein. Chain: c, d.

Source:

Klebsiella pneumoniae. Organism_taxid: 573. Gene: kpc-2, blakpc-2. Expressed in: escherichia coli. Expression_system_taxid: 562. Streptomyces clavuligerus. Organism_taxid: 1901.

Resolution:

2.10Å R-factor: 0.193 R-free: 0.234

Authors:

M.S.Hanes,K.M.Jude,J.M.Berger,R.A.Bonomo,T.M.Handel

Key ref:

M.S.Hanes et al. (2009). Structural and biochemical characterization of the interaction between KPC-2 beta-lactamase and beta-lactamase inhibitor protein. Biochemistry, 48, 9185-9193. PubMed id: 19731932

Date:

05-Aug-08 Release date: 04-Aug-09

Protein chains

Q9F663  (BLKPC_KLEPN) -  Carbapenem-hydrolyzing beta-lactamase KPC from Klebsiella pneumoniae

Seq: 293 a.a.

Struc: 261 a.a.*

Protein chains

P35804  (BLIP_STRCL) -  Beta-lactamase inhibitory protein from Streptomyces clavuligerus

Seq: 201 a.a.

Struc: 160 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B: 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+)

Biochemistry 48:9185-9193 (2009)

PubMed id: 19731932

Structural and biochemical characterization of the interaction between KPC-2 beta-lactamase and beta-lactamase inhibitor protein.

M.S.Hanes, K.M.Jude, J.M.Berger, R.A.Bonomo, T.M.Handel.

ABSTRACT

KPC beta-lactamases hydrolyze the "last resort" beta-lactam antibiotics (carbapenems) used to treat multidrug resistant infections and are compromising efforts to combat life-threatening Gram-negative bacterial infections in hospitals worldwide. Consequently, the development of novel inhibitors is essential for restoring the effectiveness of existing antibiotics. The beta-lactamase inhibitor protein (BLIP) is a competitive inhibitor of a number of class A beta-lactamases. In this study, we characterize the previously unreported interaction between KPC-2 beta-lactamase and BLIP. Biochemical results show that BLIP is an extremely potent inhibitor of KPC enzymes, binding KPC-2 and KPC-3 with subnanomolar affinity. To understand the basis of affinity and specificity in the beta-lactamase-BLIP system, the crystallographic structure of the KPC-2-BLIP complex was determined to 1.9 A resolution. Computational alanine scanning was also conducted to identify putative hot spots in the KPC-2-BLIP interface. Interestingly, the two complexes making up the KPC-2-BLIP asymmetric unit are distinct, and in one structure, the BLIP F142 loop is absent, in contrast to homologous structures in which it occupies the active site. This finding and other sources of structural plasticity appear to contribute to BLIP's promiscuity, enabling it to respond to mutations at the beta-lactamase interface. Given the continuing emergence of antibiotic resistance, the high-resolution KPC-2-BLIP structure will facilitate its use as a template for the rational design of new inhibitors of this problematic enzyme.