6SLB

Crystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.168 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase/carnithine racemaseA [auth AAA]257Thermus thermophilus JL-18Mutation(s): 0 
Gene Names: TtJL18_0099
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T3D (Subject of Investigation/LOI)
Query on T3D

Download Ideal Coordinates CCD File 
B [auth AAA](~{E})-6-[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]ethylsulfanyl]-6-oxidanylidene-hex-3-enoic acid
C27 H42 N7 O19 P3 S
VYSXESTVCZRDBA-ZPJAMBCCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.168 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.024α = 90
b = 88.024β = 90
c = 88.024γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

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