6M7G | pdb_00006m7g

Crystal structure of ArsN, N-acetyltransferase with substrate phosphinothricin from Pseudomonas putida KT2440


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 
    0.273 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Arsinothricin, an arsenic-containing non-proteinogenic amino acid analog of glutamate, is a broad-spectrum antibiotic.

Nadar, V.S.Chen, J.Dheeman, D.S.Galvan, A.E.Yoshinaga-Sakurai, K.Kandavelu, P.Sankaran, B.Kuramata, M.Ishikawa, S.Rosen, B.P.Yoshinaga, M.

(2019) Commun Biol 2: 131-131

  • DOI: https://doi.org/10.1038/s42003-019-0365-y
  • Primary Citation Related Structures: 
    5JTF, 5WPH, 6M7G

  • PubMed Abstract: 

    The emergence and spread of antimicrobial resistance highlights the urgent need for new antibiotics. Organoarsenicals have been used as antimicrobials since Paul Ehrlich's salvarsan. Recently a soil bacterium was shown to produce the organoarsenical arsinothricin. We demonstrate that arsinothricin, a non-proteinogenic analog of glutamate that inhibits glutamine synthetase, is an effective broad-spectrum antibiotic against both Gram-positive and Gram-negative bacteria, suggesting that bacteria have evolved the ability to utilize the pervasive environmental toxic metalloid arsenic to produce a potent antimicrobial. With every new antibiotic, resistance inevitably arises. The arsN1 gene, widely distributed in bacterial arsenic resistance ( ars ) operons, selectively confers resistance to arsinothricin by acetylation of the α-amino group. Crystal structures of ArsN1 N -acetyltransferase, with or without arsinothricin, shed light on the mechanism of its substrate selectivity. These findings have the potential for development of a new class of organoarsenical antimicrobials and ArsN1 inhibitors.


  • Organizational Affiliation
    • 1Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL 33199 USA.

Macromolecule Content 

  • Total Structure Weight: 282.02 kDa 
  • Atom Count: 16,138 
  • Modeled Residue Count: 2,109 
  • Deposited Residue Count: 2,484 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphinothricin N-acetyltransferase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
207Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: PP_1924
UniProt
Find proteins for Q88LK7 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88LK7 
Go to UniProtKB:  Q88LK7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88LK7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.841α = 90
b = 142.693β = 89.99
c = 178.308γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesR37 GM55425

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description