8B26 | pdb_00008b26

Dihydroprecondylocarpine acetate synthase 2 from Tabernanthe iboga

• PDB DOI: https://doi.org/10.2210/pdb8B26/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Tabernanthe iboga
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-13 Released: 2022-10-19 
• Deposition Author(s): Langley, C., Basquin, J., Caputi, L., O'Connor, S.E.
• Funding Organization(s): Max Planck Society, European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.258 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism.

Langley, C., Tatsis, E., Hong, B., Nakamura, Y., Paetz, C., Stevenson, C.E.M., Basquin, J., Lawson, D.M., Caputi, L., O'Connor, S.E.

(2022) Angew Chem Int Ed Engl 61: e202210934-e202210934

• PubMed: 36198083 
• DOI: https://doi.org/10.1002/anie.202210934
• Primary Citation Related Structures: 
  8A3N, 8B1V, 8B25, 8B26, 8B27


• PubMed Abstract: 
  

  Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.

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Organizational Affiliation: 
• Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll Straße 8, Jena, 07745, Germany.
Chinese Academy of Sciences Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, 300 Feng Lin Road, Shanghai, 200032, China.
Research Group Biosynthesis and NMR, Max Planck Institute for Chemical Ecology, Hans-Knöll Straße 8, Jena, 07745, Germany.
Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
Department of Structural Cell Biology, Max-Planck Institute for Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Planegg, Germany.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 78.69 kDa 
• Atom Count: 5,310 
• Modeled Residue Count: 717 
• Deposited Residue Count: 730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroprecondylocarpine acetate synthase 2	A, B	365	Tabernanthe iboga	Mutation(s): 0  EC: 1.3.1.128
UniProt
Find proteins for A0A5B8X8Z0 (Tabernanthe iboga) Explore A0A5B8X8Z0  Go to UniProtKB:  A0A5B8X8Z0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.258 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.422	α = 90
b = 78.124	β = 90
c = 131.207	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Langley, C., Basquin, J., Caputi, L., O'Connor, S.E.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
European Research Council (ERC)	European Union	788301

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2022-11-30
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description