5OE4 | pdb_00005oe4

Crystal structure of the N-terminal domain of PqsA in complex with anthraniloyl-AMP (crystal form 2)

• PDB DOI: https://doi.org/10.2210/pdb5OE4/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-07 Released: 2017-09-06 
• Deposition Author(s): Witzgall, F., Ewert, W., Blankenfeldt, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.250 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis.

Witzgall, F., Ewert, W., Blankenfeldt, W.

(2017) Chembiochem 18: 2045-2055

• PubMed: 28834007 
• DOI: https://doi.org/10.1002/cbic.201700374
• Primary Citation Related Structures: 
  5OE3, 5OE4, 5OE5, 5OE6


• PubMed Abstract: 
  

  Pseudomonas aeruginosa, a prevalent pathogen in nosocomial infections and a major burden in cystic fibrosis, uses three interconnected quorum-sensing systems to coordinate virulence processes. At variance with other Gram-negative bacteria, one of these systems relies on 2-alkyl-4(1H)-quinolones (Pseudomonas quinolone signal, PQS) and might hence be an attractive target for new anti-infective agents. Here we report crystal structures of the N-terminal domain of anthranilate-CoA ligase PqsA, the first enzyme of PQS biosynthesis, in complex with anthraniloyl-AMP and with 6-fluoroanthraniloyl-AMP (6FABA-AMP) at 1.4 and 1.7 Å resolution. We find that PqsA belongs to an unrecognized subfamily of anthranilate-CoA ligases that recognize the amino group of anthranilate through a water-mediated hydrogen bond. The complex with 6FABA-AMP explains why 6FABA, an inhibitor of PQS biosynthesis, is a good substrate of PqsA. Together, our data might pave a way to new pathoblockers in P. aeruginosa infections.

---

Organizational Affiliation: 
• Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany.
Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.72 kDa 
• Atom Count: 6,879 
• Modeled Residue Count: 771 
• Deposited Residue Count: 814 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate--CoA ligase	A, B	407	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: pqsA, PA0996 EC: 6.2.1.32
UniProt
Find proteins for Q9I4X3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4X3  Go to UniProtKB:  Q9I4X3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UK (Subject of Investigation/LOI)	C [auth A], D [auth B]	5'-O-[(S)-[(2-aminobenzoyl)oxy](hydroxy)phosphoryl]adenosine C17 H19 N6 O8 P XZXXWUQOHYJTTC-XNIJJKJLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.250 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.798	α = 90
b = 71.966	β = 116.9
c = 84.417	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Witzgall, F., Ewert, W., Blankenfeldt, W.

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description