8R0D | pdb_00008r0d

Crystal structure of Borneoldehydrogenase ancestor N39

• PDB DOI: https://doi.org/10.2210/pdb8R0D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-10-31 Released: 2024-10-09 
• Deposition Author(s): Helmer, C.P.O., Teijeiro-Juiz, R., Dimos, N., Loll, B.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Deciphering the evolutionary origin of the enantioselectivity of short-chain dehydrogenases from plants toward 1-borneol.

Zuson, J., Helmer, C.P.O., Di Geronimo, B., Chanique, A.M., Kavciakova, K., Teijeiro-Juiz, R., Brickel, S., Ramirez Molina, N., Drienovska, I., Kracher, D., Gaucher, E.A., Kamerlin, S.C.L., Loll, B., Kourist, R.

(2026) Nat Commun 17

• PubMed: 42744776 
• DOI: https://doi.org/10.1038/s41467-026-76435-1
• Primary Citation Related Structures: 
  8R0C, 8R0D


• PubMed Abstract: 
  

  Enzyme engineering has produced numerous methods to optimize enzymes for biotechnological processes; however, less is known about how natural evolution creates new functionalities. We investigate the evolutionary emergence of enantioselectivity in plant borneol dehydrogenases, which feature hydrophobic active-sites and are enantioselective towards dibornane-type monoterpenols. Ancestral sequence reconstruction provided a trajectory from the oldest unselective ancestor N30 (E = 12) toward a more recent selective ancestor N32, involving 19 mutations: 18 mutations are peripheral, one (I111L) occurs in the active-site. The mutation L111I in the hydrophobic pocket increased the selectivity of N30, while the back-mutation I111L decreased the selectivity of N32. Additional peripheral mutations (V136L/G169A/V183I) were required for high selectivity. Crystal structures suggested that protein dynamics rather than structural changes shape these catalytic properties; this was confirmed by Machine Learning/Molecular Mechanics simulations of ligand binding. Funnel-metadynamics simulations revealed a correlation between the active-site's solvent-accessible surface area and selectivity. This potential evolutionary pathway shapes enantioselectivity, and guides future enzyme engineering campaigns.

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Organizational Affiliation: 
• Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria.
Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
Department of Biology, Georgia State University, Atlanta, GA, USA.
Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
BioTechMed-Graz, Graz, Austria.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA. [e-mail].
School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA. [e-mail].
Department of Chemistry, Lund University, Lund, Sweden. [e-mail].
Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany. [e-mail].
Institute of Molecular Biotechnology, Graz University of Technology, Graz, Austria. [e-mail].
BioTechMed-Graz, Graz, Austria. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.14 kDa 
• Atom Count: 2,128 
• Modeled Residue Count: 251 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Borneoldehydrogenase	A	285	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	I [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.210 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m38r0d

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.89	α = 90
b = 85.52	β = 90
c = 109.72	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Helmer, C.P.O., Teijeiro-Juiz, R., Dimos, N., Loll, B.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	RTG 2473-1

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release
  
• Version 1.1: 2026-06-03
  Changes: Database references, Structure summary
• Version 1.2: 2026-09-23
  Changes: Database references