3W4Q

Crystal structure of PenA beta-lactamase from Burkholderia multivorans at pH4.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into beta-lactamases from Burkholderia species, two phylogenetically related yet distinct resistance determinants

Papp-Wallace, K.M.Taracila, M.A.Gatta, J.A.Ohuchi, N.Bonomo, R.A.Nukaga, M.

(2013) J.Biol.Chem. 288: 19090-19102

  • DOI: 10.1074/jbc.M113.458315
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Burkholderia cepacia complex and Burkholderia pseudomallei are opportunistic human pathogens. Resistance to β-lactams among Burkholderia spp. is attributable to expression of β-lactamases (e.g. PenA in B. cepacia complex and PenI in B. pseudomallei). ...

    Burkholderia cepacia complex and Burkholderia pseudomallei are opportunistic human pathogens. Resistance to β-lactams among Burkholderia spp. is attributable to expression of β-lactamases (e.g. PenA in B. cepacia complex and PenI in B. pseudomallei). Phylogenetic comparisons reveal that PenA and PenI are highly related. However, the analyses presented here reveal that PenA is an inhibitor-resistant carbapenemase, most similar to KPC-2 (the most clinically significant serine carbapenemase), whereas PenI is an extended spectrum β-lactamase. PenA hydrolyzes β-lactams with k(cat) values ranging from 0.38 ± 0.04 to 460 ± 46 s(-1) and possesses high k(cat)/k(inact) values of 2000, 1500, and 75 for β-lactamase inhibitors. PenI demonstrates the highest kcat value for cefotaxime of 9.0 ± 0.9 s(-1). Crystal structure determination of PenA and PenI reveals important differences that aid in understanding their contrasting phenotypes. Changes in the positioning of conserved catalytic residues (e.g. Lys-73, Ser-130, and Tyr-105) as well as altered anchoring and decreased occupancy of the deacylation water explain the lower k(cat) values of PenI. The crystal structure of PenA with imipenem docked into the active site suggests why this carbapenem is hydrolyzed and the important role of Arg-220, which was functionally confirmed by mutagenesis and biochemical characterization. Conversely, the conformation of Tyr-105 hindered docking of imipenem into the active site of PenI. The structural and biochemical analyses of PenA and PenI provide key insights into the hydrolytic mechanisms of β-lactamases, which can lead to the rational design of novel agents against these pathogens.


    Organizational Affiliation

    Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B, C
258Burkholderia multivorans (strain ATCC 17616 / 249)Mutation(s): 0 
Gene Names: ampC
EC: 3.5.2.6
Find proteins for A0A0H3KN52 (Burkholderia multivorans (strain ATCC 17616 / 249))
Go to UniProtKB:  A0A0H3KN52
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 121.017α = 90.00
b = 69.910β = 90.00
c = 84.350γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
SHELXL-97refinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references