6JST

Structure of Geobacillus kaustophilus lactonase, Y99P/D266N double mutant with bound 3-oxo-C8-HSL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily.

Go, M.K.Zhao, L.N.Xue, B.Supekar, S.Robinson, R.C.Fan, H.Yew, W.S.

(2020) Structure 28: 635

  • DOI: https://doi.org/10.1016/j.str.2020.03.011
  • Primary Citation of Related Structures:  
    6JSS, 6JST, 6JSU

  • PubMed Abstract: 

    In this work, we present a generalizable directed computational evolution protocol to effectively reduce the sequence space to be explored in rational enzyme design. The protocol involves in silico mutation modeling and substrate docking to rapidly identify mutagenesis hotspots that may enhance an enzyme's substrate binding and overall catalysis. By applying this protocol to a quorum-quenching Geobacillus kaustophilus lactonase, GKL, we generated 1,881 single mutants and docked high-energy intermediates of nine acyl homoserine lactones onto them. We found that Phe28 and Tyr99 were two hotspots that produced most of the predicted top 20 mutants. Of the 180 enzyme-substrate combinations (top 20 mutants × 9 substrates), 51 (28%) exhibited enhanced substrate binding and 22 (12%) had better overall activity when compared with wild-type GKL. X-ray crystallographic studies of Y99C and Y99P provided rationalized explanations for the enhancement in enzyme function and corroborated the utility of the protocol.


  • Organizational Affiliation

    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation, 14 Medical Drive, Singapore 117599, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphotriesterase
A, B, C, D
330Geobacillus kaustophilus HTA426Mutation(s): 2 
Gene Names: GK1506
EC: 3.5
UniProt
Find proteins for Q5KZU5 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KZU5 
Go to UniProtKB:  Q5KZU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KZU5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LAE
Query on LAE

Download Ideal Coordinates CCD File 
H [auth A]3-OXO-OCTANOIC ACID (2-OXO-TETRAHYDRO-FURAN-3-YL)-AMIDE
C12 H19 N O4
FXCMGCFNLNFLSH-JTQLQIEISA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
OH
Query on OH

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C]
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.991α = 90.99
b = 51.187β = 91.33
c = 134.473γ = 96.33
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)Singapore--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-06-17
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description