6RA3

Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqDC in complex with its product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Structural basis for recognition and ring-cleavage of the Pseudomonas quinolone signal (PQS) by AqdC, a mycobacterial dioxygenase of the alpha / beta-hydrolase fold family.

Wullich, S.C.Kobus, S.Wienhold, M.Hennecke, U.Smits, S.H.J.Fetzner, S.

(2019) J Struct Biol 207: 287-294

  • DOI: https://doi.org/10.1016/j.jsb.2019.06.006
  • Primary Citation of Related Structures:  
    6RA2, 6RA3, 6RB3

  • PubMed Abstract: 

    The cofactor-less dioxygenase AqdC of Mycobacteroides abscessus catalyzes the cleavage and thus inactivation of the Pseudomonas quinolone signal (PQS, 2-heptyl-3-hydroxy-4(1H)-quinolone), which plays a central role in the regulation of virulence factor production by Pseudomonas aeruginosa. We present here the crystal structures of AqdC in its native state and in complex with the PQS cleavage product N-octanoylanthranilic acid, and of mutant AqdC proteins in complex with PQS. AqdC possesses an α/β-hydrolase fold core domain with additional helices forming a cap domain. The protein is traversed by a bipartite tunnel, with a funnel-like entry section leading to an elliptical substrate cavity where PQS positioning is mediated by a combination of hydrophobic interactions and hydrogen bonds, with the substrate's C4 carbonyl and C3 hydroxyl groups tethered by His97 and the catalytic His246, respectively. The side chain of the AqdC-bound product extends deeper into the "alkyl tail section" of the tunnel than PQS, tentatively suggesting product exit via this part of the tunnel. AqdC prefers PQS over congeners with shorter alkyl substituents at C2. Kinetic data confirmed the strict requirement of the active-site base His246 for catalysis, and suggested that evolution of the canonical nucleophile/His/Asp catalytic triad of the hydrolases to an Ala/His/Asp triad is favorable for catalyzing dioxygenolytic PQS ring cleavage.


  • Organizational Affiliation

    Institute for Molecular Microbiology and Biotechnology, University of Münster, Corrensstraße 3, 48149 Münster, Germany. Electronic address: wullich@wwu.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative dioxygenase (1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase)A,
B [auth F],
C [auth E]
269Mycobacteroides abscessus subsp. abscessusMutation(s): 0 
Gene Names: SAMEA2070698_02780SAMEA2161603_04096SAMEA2275805_05965
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JWH
Query on JWH

Download Ideal Coordinates CCD File 
D [auth E]2-(octanoylamino)benzoic acid
C15 H21 N O3
DIBJPKPIMHBNDD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.173α = 90
b = 96.173β = 90
c = 189.616γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-29
    Changes: Refinement description
  • Version 2.0: 2020-06-24
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description