9IGL | pdb_00009igl

Crystal structure of P. syringae phosphinothricin acetyltransferase PSPTO_3321 in complex with L-phosphinothricin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.249 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Literature

Structure and activity of a phosphinothricin N-acetyltransferase (PSPTO_3321) from Pseudomonas syringae pv. tomato DC3000.

Davies, A.M.Trentham, D.Sutton, B.J.Brown, P.R.

(2025) Biochem Biophys Res Commun 755: 151539-151539

  • DOI: https://doi.org/10.1016/j.bbrc.2025.151539
  • Primary Citation of Related Structures:  
    9IGK, 9IGL

  • PubMed Abstract: 

    Phosphinothricin inhibits plant glutamine synthetase and is used as a herbicide. Streptomyces hygroscopicus and Streptomyces viridochromogenes, which produce phosphinothricin naturally, encode acetyltransferases that confer phosphinothricin resistance. In the Pseudomonas genome database, a number of proteins have been annotated as phosphinothricin acetyltransferases and putative phosphinothricin acetyltransferases. One such protein is PSPTO_3321 from P. syringae, a strain that causes tomato speck. Here, we reveal that PSPTO_3321 from P. syringae, termed syr_pat, is a phosphinothricin acetyltransferase, and also retains a lower level of activity against the structurally similar substrate methionine sulfoximine. We solved a 1.6 Å resolution crystal structure of syr_pat alone and a 2.5 Å resolution structure for a complex with L -phosphinothricin. We also characterised active site mutants, providing insights into substrate specificity. Our work now provides a basis for further study of the reaction mechanism.


  • Organizational Affiliation

    King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London, SE1 1UL, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphinothricin N-acetyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H
187Pseudomonas syringae pv. tomato str. DC3000Mutation(s): 0 
Gene Names: barPSPTO_3321
UniProt
Find proteins for Q87ZV1 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000))
Explore Q87ZV1 
Go to UniProtKB:  Q87ZV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87ZV1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PPQ (Subject of Investigation/LOI)
Query on PPQ

Download Ideal Coordinates CCD File 
AA [auth F]
HA [auth H]
IA [auth H]
J [auth A]
M [auth B]
AA [auth F],
HA [auth H],
IA [auth H],
J [auth A],
M [auth B],
O [auth C],
S [auth D],
W [auth E]
PHOSPHINOTHRICIN
C5 H12 N O4 P
IAJOBQBIJHVGMQ-BYPYZUCNSA-N
PEG
Query on PEG

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FA [auth G]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

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BA [auth G]
GA [auth H]
I [auth A]
L [auth B]
N [auth C]
BA [auth G],
GA [auth H],
I [auth A],
L [auth B],
N [auth C],
R [auth D],
U [auth E],
V [auth E],
Y [auth F],
Z [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

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EA [auth G],
JA [auth H],
T [auth D],
X [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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CA [auth G],
DA [auth G],
K [auth A],
P [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

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Q [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.249 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.577α = 90
b = 97.596β = 111.19
c = 117.588γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Database references