4J5N

Crystal Structure of a Deinococcus radiodurans PTE-like lactonase (drPLL) mutant Y28L/D71N/E101G/E179D/V235L/L270M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template.

Meier, M.M.Rajendran, C.Malisi, C.Fox, N.G.Xu, C.Schlee, S.Barondeau, D.P.Hocker, B.Sterner, R.Raushel, F.M.

(2013) J Am Chem Soc 135: 11670-11677

  • DOI: https://doi.org/10.1021/ja405911h
  • Primary Citation of Related Structures:  
    4J2M, 4J35, 4J5N

  • PubMed Abstract: 

    Rapid evolution of enzymes provides unique molecular insights into the remarkable adaptability of proteins and helps to elucidate the relationship between amino acid sequence, structure, and function. We interrogated the evolution of the phosphotriesterase from Pseudomonas diminuta (PdPTE), which hydrolyzes synthetic organophosphates with remarkable catalytic efficiency. PTE is thought to be an evolutionarily "young" enzyme, and it has been postulated that it has evolved from members of the phosphotriesterase-like lactonase (PLL) family that show promiscuous organophosphate-degrading activity. Starting from a weakly promiscuous PLL scaffold (Dr0930 from Deinococcus radiodurans ), we designed an extremely efficient organophosphate hydrolase (OPH) with broad substrate specificity using rational and random mutagenesis in combination with in vitro activity screening. The OPH activity for seven organophosphate substrates was simultaneously enhanced by up to 5 orders of magnitude, achieving absolute values of catalytic efficiencies up to 10(6) M(-1) s(-1). Structural and computational analyses identified the molecular basis for the enhanced OPH activity of the engineered PLL variants and demonstrated that OPH catalysis in PdPTE and the engineered PLL differ significantly in the mode of substrate binding.


  • Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphotriesterase, putative323Deinococcus radioduransMutation(s): 6 
Gene Names: Dr0930 (gi 15805954)DR_0930
UniProt
Find proteins for Q9RVU2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RVU2 
Go to UniProtKB:  Q9RVU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RVU2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.235 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.655α = 90
b = 61.655β = 90
c = 203.67γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
XFITdata reduction
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection