6D3G

PER-2 class A extended-spectrum beta-lactamase crystal structure in complex with avibactam at 2.4 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Literature

Structural Insights into the Inhibition of the Extended-Spectrum beta-Lactamase PER-2 by Avibactam.

Ruggiero, M.Papp-Wallace, K.M.Brunetti, F.Barnes, M.D.Bonomo, R.A.Gutkind, G.Klinke, S.Power, P.

(2019) Antimicrob Agents Chemother 63

  • DOI: 10.1128/AAC.00487-19
  • Primary Citation of Related Structures:  
    6D3G, 6DGU

  • PubMed Abstract: 
  • The diazabicyclooctane (DBO) avibactam (AVI) reversibly inactivates most serine-β-lactamases. Previous investigations showed that inhibition constants of AVI toward class A PER-2 are reminiscent of values observed for class C and D β-lactamases (i.e., k 2 / K of ≈10 3 M -1 s -1 ) but lower than other class A β-lactamases (i ...

    The diazabicyclooctane (DBO) avibactam (AVI) reversibly inactivates most serine-β-lactamases. Previous investigations showed that inhibition constants of AVI toward class A PER-2 are reminiscent of values observed for class C and D β-lactamases (i.e., k 2 / K of ≈10 3 M -1 s -1 ) but lower than other class A β-lactamases (i.e., k 2 / K = 10 4 to 10 5 M -1 s -1 ). Herein, biochemical and structural studies were conducted with PER-2 and AVI to explore these differences. Furthermore, biochemical studies on Arg220 and Thr237 variants with AVI were conducted to gain deeper insight into the mechanism of PER-2 inactivation. The main biochemical and structural observations revealed the following: (i) both amino-acid substitutions in Arg220 and the rich hydrophobic content in the active site hinder the binding of catalytic waters and acylation, impairing AVI inhibition; (ii) movement of Ser130 upon binding of AVI favors the formation of a hydrogen bond with the sulfate group of AVI; and (iii) the Thr237Ala substitution alters the AVI inhibition constants. The acylation constant ( k 2 / K ) of PER-2 by AVI is primarily influenced by stabilizing hydrogen bonds involving AVI and important residues such as Thr237 and Arg220. (Variants in Arg220 demonstrate a dramatic reduction in k 2 / K ) We also observed that displacement of Ser130 side chain impairs AVI acylation, an observation not made in other extended-spectrum β-lactamases (ESBLs). Comparatively, relebactam combined with a β-lactam is more potent against Escherichia coli producing PER-2 variants than β-lactam-AVI combinations. Our findings provide a rationale for evaluating the utility of the currently available DBO inhibitors against unique ESBLs like PER-2 and anticipate the effectiveness of these inhibitors toward variants that may eventually be selected upon AVI usage.


    Organizational Affiliation

    Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA, B, C, D284Citrobacter freundiiMutation(s): 0 
Gene Names: blaPER-2
EC: 3.5.2.6
UniProt
Find proteins for A2RP81 (Citrobacter freundii)
Explore A2RP81 
Go to UniProtKB:  A2RP81
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NXL (Subject of Investigation/LOI)
Query on NXL

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], H [auth C], I [auth D](2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.16α = 90
b = 85.84β = 90
c = 161.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ANPCYTArgentinaPICT-2004-0457
FONCYTArgentinaPPL-2011-2-0003

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references