6LC8 | pdb_00006lc8

Crystal structure of AmpC Ent385 complex form with avibactam

  • Classification: HYDROLASE
  • Organism(s): Enterobacter cloacae
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-11-18 Released: 2020-04-22 
  • Deposition Author(s): Kawai, A., Doi, Y.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.170 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Structural Basis of Reduced Susceptibility to Ceftazidime-Avibactam and Cefiderocol inEnterobacter cloacaeDue to AmpC R2 Loop Deletion.

Kawai, A.McElheny, C.L.Iovleva, A.Kline, E.G.Sluis-Cremer, N.Shields, R.K.Doi, Y.

(2020) Antimicrob Agents Chemother 64

  • DOI: https://doi.org/10.1128/AAC.00198-20
  • Primary Citation of Related Structures:  
    6LC7, 6LC8, 6LC9

  • PubMed Abstract: 

    Ceftazidime-avibactam and cefiderocol are two of the latest generation β-lactam agents that possess expanded activity against highly drug-resistant bacteria, including carbapenem-resistant Enterobacterales Here, we show that structural changes in AmpC β-lactamases can confer reduced susceptibility to both agents. A multidrug-resistant Enterobacter cloacae clinical strain (Ent385) was found to be resistant to ceftazidime-avibactam and cefiderocol without prior exposure to either agent. The AmpC β-lactamase of Ent385 (AmpC Ent385 ) contained an alanine-proline deletion at positions 294 and 295 (A294_P295del) in the R2 loop. AmpC Ent385 conferred reduced susceptibility to ceftazidime-avibactam and cefiderocol when cloned into Escherichia coli TOP10. Purified AmpC Ent385 showed increased hydrolysis of ceftazidime and cefiderocol compared to AmpC Ent385Rev , in which the deletion was reverted. Comparisons of crystal structures of AmpC Ent385 and AmpC P99 , the canonical AmpC of E. cloacae complex, revealed that the two-residue deletion in AmpC Ent385 induced drastic structural changes of the H-9 and H-10 helices and the R2 loop, which accounted for the increased hydrolysis of ceftazidime and cefiderocol. The potential for a single mutation in ampC to confer reduced susceptibility to both ceftazidime-avibactam and cefiderocol requires close monitoring.


  • Organizational Affiliation

    Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
360Enterobacter cloacaeMutation(s): 0 
Gene Names: CKO00_24250
EC: 3.5.2.6
UniProt
Find proteins for A0A0A0Q7Z8 (Enterobacter cloacae)
Explore A0A0A0Q7Z8 
Go to UniProtKB:  A0A0A0Q7Z8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A0Q7Z8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL (Subject of Investigation/LOI)
Query on NXL

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DIO
Query on DIO

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
R [auth B],
S [auth B]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.418α = 90
b = 73.672β = 94.49
c = 102.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NXLClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI104895
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI135522

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references
  • Version 1.2: 2020-07-08
    Changes: Database references
  • Version 1.3: 2022-03-23
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary