9KHQ | pdb_00009khq

Crystal structure of N-acyl homoserine lactonase AhlX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.210 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

An AHL-lactonase mutant featuring a unique "tri-His" motif exhibits enhanced activity, stability and effectively controls plant soft rot.

Chen, Y.Xie, X.Zhou, J.Dai, L.Chu, X.Liu, P.

(2025) Int J Biol Macromol 308: 142543-142543

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.142543
  • Primary Citation of Related Structures:  
    9KHO, 9KHQ

  • PubMed Abstract: 

    Quorum quenching through AHL-lactonase has been established as a critical approach for managing quorum sensing-mediated bacterial infections. While numerous studies have concentrated on enhancing the activity of AHL lactonases, concurrent improvements in both activity and stability have remained elusive. In this study, we adopted a hybrid strategy involving rational and semirational design to concurrently increase the activity and stability of the marine AHL-lactonase AhlX. The mutant M41 (E77I/D157G/T243Y/H255L) exhibited a significant increase in catalytic efficiency, with an 11-fold increase in k cat /K m , as well as a substantial increase in thermal stability, with a 12 °C increase in the melting temperature and a 0.6-fold longer half-life at 70 °C relative to those of wild-type AhlX. Structural insights from crystallographic analysis revealed a unique "tri-His" motif within the homohexamer that is pivotal for its stability. Removal of the "tri-His" motif from the homohexamer rendered the H158A mutant prone to thermal oligomer disassembly. Incorporation of the D157G mutation disrupted the D157-R122 salt bridge, stabilizing this motif. The T243Y and H255L mutations modify the active site conformation by reshaping surface interactions, enhancing both enzymatic activity and stability. Biocontrol experiments revealed that M41 was highly effective at suppressing potato soft rot caused by Pectobacterium carotovorum, primarily by inhibiting the swimming motility of the bacterium. This work not only deepens our understanding of the structure-activity relationships of AHL-lactonases but also lays a solid theoretical foundation for the engineering of these enzymes for biocontrol applications.


  • Organizational Affiliation
    • Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014; PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acylhomoserine lactonase
A, B, C
261Salinicola salariusMutation(s): 0 
Gene Names: ahlX
EC: 3.1.1.81
UniProt
Find proteins for A0A455K4F1 (Salinicola salarius)
Explore A0A455K4F1 
Go to UniProtKB:  A0A455K4F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A455K4F1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI (Subject of Investigation/LOI)
Query on NI

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth B]
G [auth B]
H [auth C]
D [auth A],
E [auth A],
F [auth B],
G [auth B],
H [auth C],
I [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
J [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.141α = 90
b = 143.141β = 90
c = 85.053γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaGZC20232364

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release