6OBT | pdb_00006obt

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases

• PDB DOI: https://doi.org/10.2210/pdb6OBT/pdb

• Classification: LYASE
• Organism(s): Streptomyces parvulus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-21 Released: 2019-06-05 
• Deposition Author(s): McAndrew, R.P., Barajas, J.F., Pereira, J.H., Keasling, J.D., Adams, P.D.
• Funding Organization(s): Department of Energy (DOE, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.206 (DCC) 

Starting Model: experimental

Literature

Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases.

Barajas, J.F., McAndrew, R.P., Thompson, M.G., Backman, T.W.H., Pang, B., de Rond, T., Pereira, J.H., Benites, V.T., Martin, H.G., Baidoo, E.E.K., Hillson, N.J., Adams, P.D., Keasling, J.D.

(2019) J Ind Microbiol Biotechnol 46: 1225-1235

• PubMed: 31115703 
• DOI: https://doi.org/10.1007/s10295-019-02189-z
• Primary Citation Related Structures: 
  6OBT, 6OBV


• PubMed Abstract: 
  

  Engineered polyketide synthases (PKSs) are promising synthetic biology platforms for the production of chemicals with diverse applications. The dehydratase (DH) domain within modular type I PKSs generates an α,β-unsaturated bond in nascent polyketide intermediates through a dehydration reaction. Several crystal structures of DH domains have been solved, providing important structural insights into substrate selection and dehydration. Here, we present two DH domain structures from two chemically diverse PKSs. The first DH domain, isolated from the third module in the borrelidin PKS, is specific towards a trans-cyclopentane-carboxylate-containing polyketide substrate. The second DH domain, isolated from the first module in the fluvirucin B ₁ PKS, accepts an amide-containing polyketide intermediate. Sequence-structure analysis of these domains, in addition to previously published DH structures, display many significant similarities and key differences pertaining to substrate selection. The two major differences between BorA DH M3, FluA DH M1 and other DH domains are found in regions of unmodeled residues or residues containing high B-factors. These two regions are located between α3-β11 and β7-α2. From the catalytic Asp located in α3 to a conserved Pro in β11, the residues between them form part of the bottom of the substrate-binding cavity responsible for binding to acyl-ACP intermediates.

---

Organizational Affiliation: 
• Department of Energy Agile BioFoundry, Emeryville, CA, 94608, USA.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Joint BioEnergy Institute, 5885 Hollis St. 4th Floor, Emeryville, CA, 94608, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
QB3 Institute, University of California, Berkeley, Emeryville, CA, 94608, USA.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. [e-mail].
Joint BioEnergy Institute, 5885 Hollis St. 4th Floor, Emeryville, CA, 94608, USA. [e-mail].
Department of Bioengineering, University of California, Berkeley, CA, 94720, USA. [e-mail].
QB3 Institute, University of California, Berkeley, Emeryville, CA, 94608, USA. [e-mail].
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA. [e-mail].
Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970, Horsholm, Denmark. [e-mail].
Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 33.76 kDa 
• Atom Count: 2,080 
• Modeled Residue Count: 268 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Borrelidin polyketide synthase, type I	A	314	Streptomyces parvulus	Mutation(s): 0  Gene Names: borA3
UniProt
Find proteins for Q70I00 (Streptomyces parvulus) Explore Q70I00  Go to UniProtKB:  Q70I00

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.206 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.21	α = 90
b = 63.35	β = 100.44
c = 40.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-05 
Deposition Author(s): McAndrew, R.P., Barajas, J.F., Pereira, J.H., Keasling, J.D., Adams, P.D.

---

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-05CH11231

Revision History  

• Version 1.0: 2019-06-05
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description