6BN3

CTX-M-151 class A extended-spectrum beta-lactamase apo crystal structure at 1.3 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and Biochemical Characterization of the Novel CTX-M-151 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam.

Ghiglione, B.Rodriguez, M.M.Brunetti, F.Papp-Wallace, K.M.Yoshizumi, A.Ishii, Y.Bonomo, R.A.Gutkind, G.Klinke, S.Power, P.

(2021) Antimicrob Agents Chemother 65

  • DOI: https://doi.org/10.1128/AAC.01757-20
  • Primary Citation of Related Structures:  
    6BN3, 6BPF

  • PubMed Abstract: 

    The diazabicyclooctane (DBO) inhibitor avibactam (AVI) reversibly inactivates most serine β-lactamases, including the CTX-M β-lactamases. Currently, more than 230 unique CTX-M members distributed in five clusters with less than 5% amino acid sequence divergence within each group have been described. Recently, a variant named CTX-M-151 was isolated from a Salmonella enterica subsp. enterica serovar Choleraesuis strain in Japan. This variant possesses a low degree of amino acid identity with the other CTX-Ms (63.2% to 69.7% with respect to the mature proteins), and thus it may represent a new subgroup within the family. CTX-M-151 hydrolyzes ceftriaxone better than ceftazidime ( k cat / K m values 6,000-fold higher), as observed with CTX-Ms. CTX-M-151 is well inhibited by mechanism-based inhibitors like clavulanic acid (inactivation rate [ k inact ]/inhibition constant [ K i ] = 0.15 μM -1 · s -1 ). For AVI, the apparent inhibition constant ( K i app ), 0.4 μM, was comparable to that of KPC-2; the acylation rate ( k 2 /K) (37,000 M -1 · s -1 ) was lower than that for CTX-M-15, while the deacylation rate ( k off ) (0.0015 s -1 ) was 2- to 14-fold higher than those of other class A β-lactamases. The structure of the CTX-M-151/AVI complex (1.32 Å) reveals that AVI adopts a chair conformation with hydrogen bonds between the AVI carbamate and Ser70 and Ser237 at the oxyanion hole. Upon acylation, the side chain of Lys73 points toward Ser130, which is associated with the protonation of Glu166, supporting the role of Lys73 in the proton relay pathway and Glu166 as the general base in deacylation. To our knowledge, this is the first chromosomally encoded CTX-M in Salmonella Choleraesuis that shows similar hydrolytic preference toward cefotaxime (CTX) and ceftriaxone (CRO) to that toward ceftazidime (CAZ).


  • Organizational Affiliation

    Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Laboratorio de Resistencia Bacteriana, Buenos Aires, Argentina.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase267Salmonella entericaMutation(s): 0 
Gene Names: blaCTX-M151
EC: 3.5.2.6
UniProt
Find proteins for A0A077KT80 (Salmonella enterica)
Explore A0A077KT80 
Go to UniProtKB:  A0A077KT80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077KT80
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE (Subject of Investigation/LOI)
Query on EPE

Download Ideal Coordinates CCD File 
B [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.79α = 90
b = 41.81β = 94.14
c = 56.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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: 2018-11-21
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references, Structure summary
  • Version 1.2: 2021-01-20
    Changes: Structure summary
  • Version 1.3: 2022-08-03
    Changes: Database references
  • Version 1.4: 2024-05-22
    Changes: Data collection