7TYB

Salicylate Adenylate PchD from Pseudomonas aeruginosa containing salicyl-AMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Rational inhibitor design for Pseudomonas aeruginosa salicylate adenylation enzyme PchD.

Shelton, C.L.Meneely, K.M.Ronnebaum, T.A.Chilton, A.S.Riley, A.P.Prisinzano, T.E.Lamb, A.L.

(2022) J Biol Inorg Chem 27: 541-551

  • DOI: https://doi.org/10.1007/s00775-022-01941-8
  • Primary Citation of Related Structures:  
    7TYB, 7TZ4

  • PubMed Abstract: 

    Pseudomonas aeruginosa is an increasingly antibiotic-resistant pathogen that causes severe lung infections, burn wound infections, and diabetic foot infections. P. aeruginosa produces the siderophore pyochelin through the use of a non-ribosomal peptide synthetase (NRPS) biosynthetic pathway. Targeting members of siderophore NRPS proteins is one avenue currently under investigation for the development of new antibiotics against antibiotic-resistant organisms. Here, the crystal structure of the pyochelin adenylation domain PchD is reported. The structure was solved to 2.11 Å when co-crystallized with the adenylation inhibitor 5'-O-(N-salicylsulfamoyl)adenosine (salicyl-AMS) and to 1.69 Å with a modified version of salicyl-AMS designed to target an active site cysteine (4-cyano-salicyl-AMS). In the structures, PchD adopts the adenylation conformation, similar to that reported for AB3403 from Acinetobacter baumannii.


  • Organizational Affiliation

    Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyochelin biosynthesis protein PchD547Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pchDPA4228
EC: 6.2.1.61
UniProt
Find proteins for Q9HWG3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HWG3 
Go to UniProtKB:  Q9HWG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HWG3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KT0 (Subject of Investigation/LOI)
Query on KT0

Download Ideal Coordinates CCD File 
B [auth A]5'-O-[(2-hydroxybenzoyl)sulfamoyl]adenosine
C17 H18 N6 O8 S
SABYITLYKSVAAD-CNEMSGBDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.064α = 90
b = 44.834β = 99.091
c = 67.199γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
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 General Medical Sciences (NIH/NIGMS)United StatesR01GM127655
National Science Foundation (NSF, United States)United States1904494
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK12GM063651

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description