5GWA

Crystal structure of TLA-3 extended-spectrum beta-lactamase in a complex with avibactam

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

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Literature

Structural Insights into the TLA-3 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam and OP0595.

Jin, W., Wachino, J., Yamaguchi, Y., Kimura, K., Kumar, A., Yamada, M., Morinaka, A., Sakamaki, Y., Yonezawa, M., Kurosaki, H., Arakawa, Y.

(2017) Antimicrob Agents Chemother 61

  • DOI: 10.1128/AAC.00501-17
  • Primary Citation of Related Structures:  
    5GS8, 5GWA, 5X5G

  • PubMed Abstract: 

    • The development of effective inhibitors that block extended-spectrum β-lactamases (ESBLs) and restore the action of β-lactams represents an effective strategy against ESBL-producing Enterobacteriaceae We evaluated the inhibitory effects of the diazabicyclooctanes avibactam and OP0595 against TLA-3, an ESBL that we identified previously ...

    The development of effective inhibitors that block extended-spectrum β-lactamases (ESBLs) and restore the action of β-lactams represents an effective strategy against ESBL-producing Enterobacteriaceae We evaluated the inhibitory effects of the diazabicyclooctanes avibactam and OP0595 against TLA-3, an ESBL that we identified previously. Avibactam and OP0595 inhibited TLA-3 with apparent inhibitor constants ( K i app ) of 1.71 ± 0.10 and 1.49 ± 0.05 μM, respectively, and could restore susceptibility to cephalosporins in the TLA-3-producing Escherichia coli strain. The value of the second-order acylation rate constant ( k 2 / K , where k 2 is the acylation rate constant and K is the equilibrium constant) of avibactam [(3.25 ± 0.03) × 10 3 M -1 · s -1 ] was closer to that of class C and D β-lactamases ( k 2 / K , <10 4 M -1 · s -1 ) than that of class A β-lactamases ( k 2 / K , >10 4 M -1 · s -1 ). In addition, we determined the structure of TLA-3 and that of TLA-3 complexed with avibactam or OP0595 at resolutions of 1.6, 1.6, and 2.0 Å, respectively. TLA-3 contains an inverted Ω loop and an extended loop between the β5 and β6 strands (insertion after Ser237), which appear only in PER-type class A β-lactamases. These structures might favor the accommodation of cephalosporins harboring bulky R1 side chains. TLA-3 presented a high catalytic efficiency ( k cat / K m ) against cephalosporins, including cephalothin, cefuroxime, and cefotaxime. Avibactam and OP0595 bound covalently to TLA-3 via the Ser70 residue and made contacts with residues Ser130, Thr235, and Ser237, which are conserved in ESBLs. Additionally, the sulfate group of the inhibitors formed polar contacts with amino acid residues in a positively charged pocket of TLA-3. Our findings provide a structural template for designing improved diazabicyclooctane-based inhibitors that are effective against ESBL-producing Enterobacteriaceae .

    Organizational Affiliation: 

    Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA280Serratia marcescensMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for A0A0B6VPP7 (Serratia marcescens)
Explore A0A0B6VPP7 
Go to UniProtKB:  A0A0B6VPP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B6VPP7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NXL
Query on NXL
Download Ideal Coordinates CCD File 
B [auth A](2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
Z [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.939α = 90
b = 68.12β = 94.53
c = 45.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-12
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references