Crystal structure of isomerase PaaG mutant - D136N with Oxepin-CoA

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 

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This is version 1.2 of the entry. See complete history


Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism.

Spieker, M.Saleem-Batcha, R.Teufel, R.

(2019) ACS Chem Biol 14: 2876-2886

  • DOI: https://doi.org/10.1021/acschembio.9b00742
  • Primary Citation of Related Structures:  
    6SL9, 6SLA, 6SLB

  • PubMed Abstract: 

    Numerous aromatic compounds are aerobically degraded in bacteria via the central intermediate phenylacetic acid (paa). In one of the key steps of this widespread catabolic pathway, 1,2-epoxyphenylacetyl-CoA is converted by PaaG into the heterocyclic oxepin-CoA. PaaG thereby elegantly generates an α,β-unsaturated CoA ester that is predisposed to undergo β-oxidation subsequent to hydrolytic ring-cleavage. Moreover, oxepin-CoA serves as a precursor for secondary metabolites (e.g., tropodithietic acid) that act as antibiotics and quorum-sensing signals. Here we verify that PaaG adopts a second role in aromatic catabolism by converting cis -3,4-didehydroadipoyl-CoA into trans -2,3-didehydroadipoyl-CoA and corroborate a Δ 3 2 -enoyl-CoA isomerase-like proton shuttling mechanism for both distinct substrates. Biochemical and structural investigations of PaaG reveal active site adaptations to the structurally different substrates and provide detailed insight into catalysis and control of stereospecificity. This work elucidates the mechanism of action of unusual isomerase PaaG and sheds new light on the ubiquitous enoyl-CoA isomerases of the crotonase superfamily.

  • Organizational Affiliation

    ZBSA, Center for Biological Systems Analysis , University of Freiburg , 79104 Freiburg , Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase/carnithine racemase254Thermus thermophilus JL-18Mutation(s): 1 
Gene Names: TtJL18_0099
Find proteins for H9ZNW0 (Thermus thermophilus JL-18)
Explore H9ZNW0 
Go to UniProtKB:  H9ZNW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9ZNW0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LHQ (Subject of Investigation/LOI)
Query on LHQ

Download Ideal Coordinates CCD File 
G [auth AAA]
H [auth BBB]
I [auth CCC]
J [auth DDD]
K [auth EEE]
G [auth AAA],
H [auth BBB],
I [auth CCC],
J [auth DDD],
K [auth EEE],
L [auth FFF]
~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 2-(2,5-dihydrooxepin-7-yl)ethanethioate
C29 H44 N7 O18 P3 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.156α = 90
b = 73.05β = 92.482
c = 130.304γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyTE 931/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description