8PNG | pdb_00008png

Crystal structure of the apo acyl-CoA dehydrogenase FadE2 (PA0508) from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Pseudomonas aeruginosa acyl-CoA dehydrogenases and structure-guided inversion of their substrate specificity.

Wang, M.Medarametla, P.Kronenberger, T.Deingruber, T.Brear, P.Figueroa, W.Ho, P.M.Krueger, T.Pearce, J.C.Poso, A.Wakefield, J.G.Spring, D.R.Welch, M.

(2025) Nat Commun 16: 2334-2334

  • DOI: https://doi.org/10.1038/s41467-025-57532-z
  • Primary Citation Related Structures: 
    8PNG, 8PNS, 8PU5, 8R1E

  • PubMed Abstract: 

    Fatty acids are a primary source of carbon for Pseudomonas aeruginosa (PA) in the airways of people with cystic fibrosis (CF). Here, we use tandem mass-tag proteomics to analyse the protein expression profile of a CF clinical isolate grown on different fatty acids. Two fatty acyl-CoA dehydrogenases (designated FadE1 and FadE2) are strongly induced during growth on fatty acids. FadE1 displays a strong preference for long-chain acyl-CoAs, whereas FadE2 exclusively utilizes medium-chain acyl-CoAs. Structural analysis of the enzymes enables us to identify residues comprising the substrate selectivity filter in each. Engineering these residues enables us to invert the substrate specificity of each enzyme. Mutants in fadE1 displayed impaired virulence in an infection model, and decreased growth on long chain fatty acids. The unique features of the substrate binding pocket enable us to identify an inhibitor that is differentially active against FadE1 and FadE2.


  • Organizational Affiliation
    • Department of Biochemistry, Tennis Court Road, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 130.58 kDa 
  • Atom Count: 9,714 
  • Modeled Residue Count: 1,184 
  • Deposited Residue Count: 1,188 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable acyl-CoA dehydrogenaseA [auth B],
B [auth A]
594Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA0508
EC: 1.3.99.41
UniProt
Find proteins for Q9I610 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I610 
Go to UniProtKB:  Q9I610
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I610
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
C [auth B],
F [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
E [auth B],
K [auth A],
L [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth B],
G [auth A],
H [auth A],
I [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.851α = 90
b = 64.396β = 90
c = 286.967γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Xia2 DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cystic Fibrosis TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references