6KA5

Crystal structure of a class C beta-lactamase in complex with cefoxitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structural Insights into Catalytic Relevances of Substrate Poses in ACC-1.

Bae, D.W.Jung, Y.E.An, Y.J.Na, J.H.Cha, S.S.

(2019) Antimicrob Agents Chemother 63

  • DOI: https://doi.org/10.1128/AAC.01411-19
  • Primary Citation of Related Structures:  
    6K8X, 6K9T, 6KA5, 6KBY

  • PubMed Abstract: 

    ACC-1 is a plasmid-encoded class C β-lactamase identified in clinical isolates of Klebsiella pneumoniae , Proteus mirabilis , Salmonella enterica , and Escherichia coli ACC-1-producing bacteria are susceptible to cefoxitin, whereas they are resistant to oxyimino cephalosporins. Here, we depict crystal structures of apo ACC-1, adenylylated ACC-1, and acylated ACC-1 complexed with cefotaxime and cefoxitin. ACC-1 has noteworthy structural alterations in the R2 loop, the Ω loop, and the Phe119 loop located along the active-site rim. The adenylate covalently bonded to the nucleophilic serine reveals a tetrahedral phosphorus mimicking the deacylation transition state. Cefotaxime in ACC-1 has a proper conformation for the substrate-assisted catalysis in that its C-4 carboxylate and N-5 nitrogen are adequately located to facilitate the deacylation reaction. In contrast, cefoxitin in ACC-1 has a distinct conformation, in which those functional groups cannot contribute to catalysis. Furthermore, the orientation of the deacylating water relative to the acyl carbonyl group in ACC-1 is unfavorable for nucleophilic attack.


  • Organizational Affiliation

    Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase370Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla-ACC-1acc-1
EC: 3.5.2.6
UniProt
Find proteins for Q9XB24 (Klebsiella pneumoniae)
Explore Q9XB24 
Go to UniProtKB:  Q9XB24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XB24
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1S7 (Subject of Investigation/LOI)
Query on 1S7

Download Ideal Coordinates CCD File 
B [auth A](2R)-2-{(1S)-1-methoxy-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C15 H16 N2 O5 S2
BMQDZZSQSZJJQV-CABCVRRESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.092α = 90
b = 60.34β = 111.93
c = 56.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building
MOLREPphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 2.0: 2022-10-12
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
  • Version 2.1: 2023-11-29
    Changes: Data collection, Refinement description