8QNZ

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.146 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity.

Zhou, Q.Catalan, P.Bell, H.Baumann, P.Cooke, R.Evans, R.Yang, J.Zhang, Z.Zappala, D.Zhang, Y.Blackburn, G.M.He, Y.Jin, Y.

(2023) ACS Cent Sci 9: 2339-2349

  • DOI: https://doi.org/10.1021/acscentsci.3c00609
  • Primary Citation of Related Structures:  
    8QNZ

  • PubMed Abstract: 

    Antibiotic-resistant Enterobacterales that produce oxacillinase (OXA)-48-like Class D β-lactamases are often linked to increased clinical mortality. Though the catalytic mechanism of OXA-48 is known, the molecular origin of its biphasic kinetics has been elusive. We here identify selective chloride binding rather than decarbamylation of the carbamylated lysine as the source of biphasic kinetics, utilizing isothermal titration calorimetry (ITC) to monitor the complete reaction course with the OXA-48 variant having a chemically stable N -acetyl lysine. Further structural investigation enables us to capture an unprecedented inactive acyl intermediate wedged in place by a halide ion paired with a conserved active site arginine. Supported by mutagenesis and mathematical simulation, we identify chloride as a "Janus effector" that operates by allosteric activation of the burst phase and by inhibition of the steady state in kinetic assays of β-lactams. We show that chloride-induced biphasic kinetics directly affects antibiotic efficacy and facilitates the differentiation of clinical isolates encoding Class D from Class A and B carbapenemases. As chloride is present in laboratory and clinical procedures, our discovery greatly expands the roles of chloride in modulating enzyme catalysis and highlights its potential impact on the pharmacokinetics and efficacy of antibiotics during in vivo treatment.


  • Organizational Affiliation

    Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamaseA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
260Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla OXA-48bla_2blaOXA-48G5637_27540KPE71T_00045SAMEA3649466_05396
EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae)
Explore Q6XEC0 
Go to UniProtKB:  Q6XEC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XEC0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8YF (Subject of Investigation/LOI)
Query on 8YF

Download Ideal Coordinates CCD File 
E [auth AAA],
K [auth BBB],
R [auth DDD]
(2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid
C12 H19 N3 O5 S
KSLAOLVLEKIZMQ-ZXFLCMHBSA-N
BR (Subject of Investigation/LOI)
Query on BR

Download Ideal Coordinates CCD File 
F [auth AAA]
G [auth AAA]
H [auth AAA]
I [auth AAA]
J [auth AAA]
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
M [auth BBB],
N [auth BBB],
O [auth BBB],
P [auth CCC],
Q [auth CCC],
S [auth DDD]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
1BO
Query on 1BO

Download Ideal Coordinates CCD File 
L [auth BBB]1-BUTANOL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.31α = 90
b = 105.965β = 90
c = 124.679γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31400663

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-03-06
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Database references