PDBsum entry: 1ko3

Hydrolase

PDB id: 1ko3

Contents

Protein chain

230 a.a. *

Ligands

ACT ×2

_OH

Metals

_ZN ×3

_CL

Waters ×136

* Residue conservation analysis

PDB id:

1ko3

Name:

Hydrolase

Title:

Vim-2, a zn-beta-lactamase from pseudomonas aeruginosa with cys221 reduced

Structure:

Vim-2 metallo-beta-lactamase. Chain: a. Fragment: residues 30-295. Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Gene: blavim-2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.91Å R-factor: 0.209 R-free: 0.250

Authors:

I.Garcia-Saez,J.-D.Docquier,G.M.Rossolini,O.Dideberg

Key ref:

I.Garcia-Saez et al. (2008). The three-dimensional structure of VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa in its reduced and oxidised form. J Mol Biol, 375, 604-611. PubMed id: 18061205 DOI: 10.1016/j.jmb.2007.11.012

Date:

20-Dec-01 Release date: 02-Sep-03

Protein chain

Q9K2N0  (Q9K2N0_PSEAE) -  Beta-lactamase class B VIM-2

Seq: 266 a.a.

Struc: 231 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: hydrolase activity (1 term)

DOI no: 10.1016/j.jmb.2007.11.012

J Mol Biol 375:604-611 (2008)

PubMed id: 18061205

The three-dimensional structure of VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa in its reduced and oxidised form.

I.Garcia-Saez, J.D.Docquier, G.M.Rossolini, O.Dideberg.

ABSTRACT

The crystal structures of the universally widespread metallo-beta-lactamase (MBL) Verona integron-encoded MBL (VIM)-2 from Pseudomonas aeruginosa have been solved in their native form as well as in an unexpected oxidised form. This carbapenem-hydrolysing enzyme belongs to the so-called B1 subfamily of MBLs and shares the folding of alpha beta/beta alpha sandwich, consisting of a core of beta-sheet surrounded by alpha-helices. Surprisingly, it showed a high tendency to be strongly oxidised at the catalytic cysteine located in the Cys site, Cys221, which, in the oxidised structure, becomes a cysteinesulfonic residue. Its native structure was obtained only in the presence of Tris(2-carboxyethyl)phosphine. This oxidation might be a consequence of a lower affinity for the second Zn located in the Cys site that would also explain the observed susceptibility of VIM-2 to chelating agents. This modification, if present in nature, might play a role in catalytic down-regulation. Comparison between native and oxidised VIM-2 and a predicted model of VIM-1 (which shows one residue different in the Cys site compared with VIM-2) is performed to explain the different activities and antibiotic specificities.

Selected figure(s)

Figure 2.
Fig. 2. Stereo view of the active site (His and Cys sites) of (a) VIM-2 and (b) oxidised VIM-2. Contacts between the Zn ions and Cys221 [in (a)] or Ocs221 [in (b)] with residues of the active site (< 3.5 Å) are depicted. Water molecules are shown as red spheres. The asterisk symbol indicates the position of the two residues in VIM-2 (Tyr224 and Arg228) that are different in VIM-1 (His224 and Ser228).

Figure 3.
Fig. 3. Secondary structure of VIM-2 (in orange) and sequence alignment with VIM-1 and VIM-3 variants. The residues labelled in black and green are the differences between VIM-2 and VIM-1 and between VIM-2 and VIM-3, respectively. Residues labelled in red belong to the His and Cys active sites. The asterisk symbol indicates the position of the two residues that are different in VIM-1 in comparison with VIM-2 in the Cys site.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 375, 604-611) copyright 2008.

Figures were selected by an automated process.