8F9X | pdb_00008f9x

Cyclase-Phosphotriesterase from Ruegeria pomeroyi DSS-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.253 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

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


This is version 2.1 of the entry. See complete history


Literature

A Thermostable Bacterial Metallohydrolase that Degrades Organophosphate Plasticizers.

Ji, D.Frkic, R.L.Delyami, J.Larsen, J.S.Spence, M.A.Jackson, C.J.

(2025) Chembiochem 26: e202500055-e202500055

  • DOI: https://doi.org/10.1002/cbic.202500055
  • Primary Citation of Related Structures:  
    8F9X

  • PubMed Abstract: 

    A cyclase-phosphotriesterase (C-PTE) from Ruegeria pomeroyi DSS-3 has recently been identified for its capacity to detoxify several organophosphate compounds. However, several aspects of this enzyme remain unexplored, such as its activity with industrial organophosphates, its molecular structure, and its thermostability. In this work, the crystal structure of C-PTE is reported, which is solved to 2.3 Å resolution, providing insight into the enzyme's mechanism of action, revealing a binuclear Zn 2+ active site and distant similarity to other phosphotriesterases from the amidohydrolase superfamily. It is shown that C-PTE catalyzes the hydrolysis of the OP plasticizers triphenyl phosphate (TPhP) and tris(2-chloropropyl) phosphate (TCPP), albeit with low efficiency, but not the sterically bulkier tri-o-tolyl phosphate (ToTP). Finally, it is demonstrated that, even though Ruegeria pomeroyi DSS-3 is not a thermophile, C-PTE exhibits remarkable thermostability and retains structure up to 90 °C. Overall, these findings advance the understanding of C-PTE, suggesting that it is a good candidate for engineering owing to its thermostability and that it could contribute to bioremediation strategies to reduce the impact of pollution by industrial organophosphates.


  • Organizational Affiliation

    Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclase family protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
230Ruegeria pomeroyi DSS-3Mutation(s): 0 
Gene Names: SPO0761
UniProt
Find proteins for Q5LVE1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Explore Q5LVE1 
Go to UniProtKB:  Q5LVE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LVE1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTB
Query on BTB

Download Ideal Coordinates CCD File 
EB [auth H]
FA [auth D]
M [auth A]
MB [auth I]
N [auth A]
EB [auth H],
FA [auth D],
M [auth A],
MB [auth I],
N [auth A],
PA [auth F],
PB [auth I],
QA [auth F],
U [auth B],
UB [auth J],
VB [auth J],
X [auth C],
XA [auth G],
YA [auth G]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
BA [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
DB [auth H]
EA [auth D]
JA [auth E]
LB [auth I]
T [auth B]
DB [auth H],
EA [auth D],
JA [auth E],
LB [auth I],
T [auth B],
TB [auth J]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth H]
BB [auth H]
CA [auth D]
CB [auth H]
DA [auth D]
AB [auth H],
BB [auth H],
CA [auth D],
CB [auth H],
DA [auth D],
HA [auth E],
IA [auth E],
IB [auth I],
JB [auth I],
K [auth A],
KB [auth I],
L [auth A],
NA [auth F],
OA [auth F],
Q [auth B],
QB [auth J],
R [auth B],
RB [auth J],
S [auth B],
SB [auth J],
UA [auth G],
V [auth C],
VA [auth G],
W [auth C],
WA [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
FB [auth H]
GA [auth D]
GB [auth H]
HB [auth H]
AA [auth C],
FB [auth H],
GA [auth D],
GB [auth H],
HB [auth H],
KA [auth E],
LA [auth E],
MA [auth E],
NB [auth I],
O [auth A],
OB [auth I],
P [auth A],
RA [auth F],
SA [auth F],
TA [auth F],
WB [auth J],
Y [auth C],
Z [auth C],
ZA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.253 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.08α = 90
b = 68.08β = 90
c = 446.501γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaCE200100012
Australian Research Council (ARC)AustraliaCE200100029

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 2.0: 2025-01-29
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2025-06-18
    Changes: Database references