PDBsum entry: 1k56

Hydrolase

PDB id: 1k56

Contents

Protein chains

243 a.a. *

Ligands

SO4 ×6

Waters ×684

* Residue conservation analysis

PDB id:

1k56

Name:

Hydrolase

Title:

Oxa 10 class d beta-lactamase at ph 6.5

Structure:

Oxa10 beta-lactamase. Chain: a, b, c. Synonym: beta-lactamase pse-2. Engineered: yes. Other_details: residue 70 of chains a and b are kcx are car lysine. Residue 70 of chain c exists in two alternate confo kcx, carbamylated lysine, and lysine.. Oxa10 beta-lactamase. Chain: d.

Source:

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

Resolution:

1.70Å R-factor: 0.184 R-free: 0.221

Authors:

D.Golemi,L.Maveyraud,S.Vakulenko,J.P.Samama,S.Mobashery

Key ref:

D.Golemi et al. (2001). Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases. Proc Natl Acad Sci U S A, 98, 14280-14285. PubMed id: 11724923 DOI: 10.1073/pnas.241442898

Date:

10-Oct-01 Release date: 07-Nov-01

Protein chains

P14489  (BLO10_PSEAE) -  Beta-lactamase OXA-10

Seq: 266 a.a.

Struc: 243 a.a.*

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

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: peptidoglycan-based cell wall biogenesis (3 terms)
• Biochemical function: hydrolase activity (3 terms)

DOI no: 10.1073/pnas.241442898

Proc Natl Acad Sci U S A 98:14280-14285 (2001)

PubMed id: 11724923

Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases.

D.Golemi, L.Maveyraud, S.Vakulenko, J.P.Samama, S.Mobashery.

ABSTRACT

beta-Lactamases are the resistance enzymes for beta-lactam antibiotics, of which four classes are known. beta-lactamases hydrolyze the beta-lactam moieties of these antibiotics, rendering them inactive. It is shown herein that the class D OXA-10 beta-lactamase depends critically on an unusual carbamylated lysine as the basic residue for both the enzyme acylation and deacylation steps of catalysis. The formation of carbamylated lysine is reversible. Evidence is presented that this enzyme is dimeric and carbamylated in living bacteria. High-resolution x-ray structures for the native enzyme were determined at pH values of 6.0, 6.5, 7.5, and 8.5. Two dimers are present per asymmetric unit. One monomer in each dimer was carbamylated at pH 6.0, whereas all four monomers were fully carbamylated at pH 8.5. At the intermediate pH values, one monomer of each dimer was carbamylated, and the other showed a mixture of carbamylated and non-carbamylated lysines. It would appear that, as the pH increased for the sample, additional lysines were "titrated" by carbamylation. A handful of carbamylated lysines are known from protein crystallographic data, all of which have been attributed roles in structural stabilization (mostly as metal ligands) of the proteins. This paper reports a previously unrecognized role for a noncoordinated carbamylate lysine as a basic residue involved in mechanistic reactions of an enzyme, which indicates another means for expansion of the catalytic capabilities of the amino acids in nature beyond the 20 common amino acids in development of biological catalysts.

Selected figure(s)

Figure 3.
Fig. 3. Active site structure at pH 8.5 (A), pH 6.0 (B), and when Ser-67 is acylated (C). Main chain, thick lines; side chain, thin lines. Water molecules are indicated as red spheres. The additional sulfate and water molecules observed at pH 6.0 (B) and the inhibitor (C) are depicted in green.

Figure 4.
Fig. 4. Superimposition of the OXA-10 -lactamase structure when Lys-70 is carbamylated (red) and when it is not carbamylated (green).

Figures were selected by the author.