Structure of cyclohex-1-ene-1-carboxyl-CoA dehydrogenase complexed with cyclohex-1,5-diene-1-carboxyl-CoA

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Structural Basis of Cyclic 1,3-Diene Forming Acyl-Coenzyme A Dehydrogenases.

Kung, J.W.Meier, A.K.Willistein, M.Weidenweber, S.Demmer, U.Ermler, U.Boll, M.

(2021) Chembiochem 22: 3173-3177

  • DOI: https://doi.org/10.1002/cbic.202100421
  • Primary Citation of Related Structures:  
    7P98, 7P9A, 7P9X

  • PubMed Abstract: 

    The biologically important, FAD-containing acyl-coenzyme A (CoA) dehydrogenases (ACAD) usually catalyze the anti-1,2-elimination of a proton and a hydride of aliphatic CoA thioesters. Here, we report on the structure and function of an ACAD from anaerobic bacteria catalyzing the unprecedented 1,4-elimination at C3 and C6 of cyclohex-1-ene-1-carboxyl-CoA (Ch1CoA) to cyclohex-1,5-diene-1-carboxyl-CoA (Ch1,5CoA) and at C3 and C4 of the latter to benzoyl-CoA. Based on high-resolution Ch1CoA dehydrogenase crystal structures, the unorthodox reactivity is explained by the presence of a catalytic aspartate base (D91) at C3, and by eliminating the catalytic glutamate base at C1. Moreover, C6 of Ch1CoA and C4 of Ch1,5CoA are positioned towards FAD-N5 to favor the biologically relevant C3,C6- over the C3,C4-dehydrogenation activity. The C1,C2-dehydrogenation activity was regained by structure-inspired amino acid exchanges. The results provide the structural rationale for the extended catalytic repertoire of ACADs and offer previously unknown biocatalytic options for the synthesis of cyclic 1,3-diene building blocks.

  • Organizational Affiliation

    Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short-chain acyl-CoA dehydrogenase
A, B
412Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: Gmet_3306
Find proteins for Q39QF5 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39QF5 
Go to UniProtKB:  Q39QF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39QF5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4KX (Subject of Investigation/LOI)
Query on 4KX

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
1,5 Dienoyl-CoA
C28 H42 N7 O17 P3 S
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C27 H33 N9 O15 P2
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.26α = 90
b = 173.59β = 90
c = 331.54γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySPP1319 (ER 222/5-1)
German Research Foundation (DFG)GermanyRTG 1976 (235777276)

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description