Crystal structure of bifunctional dehydratase-cyclase domain in ambruticin biosynthesis

Experimental Data Snapshot

  • Resolution: 1.17 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 

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Insights into the Dual Activity of a Bifunctional Dehydratase-Cyclase Domain.

Sung, K.H.Berkhan, G.Hollmann, T.Wagner, L.Blankenfeldt, W.Hahn, F.

(2018) Angew Chem Int Ed Engl 57: 343-347

  • DOI: https://doi.org/10.1002/anie.201707774
  • Primary Citation of Related Structures:  
    5O15, 5O16

  • PubMed Abstract: 

    Oxygen-containing heterocycles are a common structural motif in polyketide natural products and contribute significantly to their biological activity. Here, we report structural and mechanistic investigations on AmbDH3, a polyketide synthase domain with dual activity as dehydratase (DH) and pyran-forming cyclase in ambruticin biosynthesis. AmbDH3 is similar to monofunctional DH domains, using H51 and D215 for dehydration. V173 was confirmed as a diagnostic residue for cyclization activity by a mutational study and enzymatic in vitro experiments. Similar motifs were observed in the seemingly monofunctional AmbDH2, which also shows an unexpected cyclase activity. Our results pave the way for mining of hidden cyclases in biosynthetic pathways. They also open interesting prospects for the generation of novel biocatalysts for chemoenzymatic synthesis and pyran-polyketides by combinatorial biosynthesis.

  • Organizational Affiliation

    Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
311Sorangium cellulosumMutation(s): 0 
Gene Names: ambC
Find proteins for A1YBQ4 (Sorangium cellulosum)
Explore A1YBQ4 
Go to UniProtKB:  A1YBQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1YBQ4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.17 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.841α = 90
b = 91.495β = 90
c = 143.689γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
autoPROCdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyHA 5841/2-1
European Union293430

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description