5O16

Crystal structure of bifunctional dehydratase-cyclase domain in ambruticin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb5O16/pdb

• Classification: LYASE
• Organism(s): Sorangium cellulosum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-18 Released: 2017-11-08 
• Deposition Author(s): Sung, K.H., Berkhan, G., Hollmann, T., Wagner, L., Hahn, F., Blankenfeldt, W.
• Funding Organization(s): German Research Foundation, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

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

• PubMed: 29084363 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS, gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.37 kDa 
• Atom Count: 4,052 
• Modelled Residue Count: 551 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmbC	A, B	311	Sorangium cellulosum	Mutation(s): 0  Gene Names: ambC
UniProt
Find proteins for A1YBQ4 (Sorangium cellulosum) Explore A1YBQ4  Go to UniProtKB:  A1YBQ4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.548	α = 90
b = 114.548	β = 90
c = 132.048	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
autoPROC	data reduction
BALBES	phasing
autoPROC	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Sung, K.H., Berkhan, G., Hollmann, T., Wagner, L., Hahn, F., Blankenfeldt, W.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	HA 5841/2-1
European Union		293430

Revision History  

• 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