Formate dehydrogenase wild-type enzyme from Candida dubliniensis complexed with NADH

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 

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Engineering a Formate Dehydrogenase for NADPH Regeneration.

Ma, W.Geng, Q.Chen, C.Zheng, Y.C.Yu, H.L.Xu, J.H.

(2023) Chembiochem 24: e202300390-e202300390

  • DOI: https://doi.org/10.1002/cbic.202300390
  • Primary Citation of Related Structures:  
    8J3O, 8J3P

  • PubMed Abstract: 

    Nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH) constitute major hydrogen donors for oxidative/reductive bio-transformations. NAD(P)H regeneration systems coupled with formate dehydrogenases (FDHs) represent a dreamful method. However, most of the native FDHs are NAD + -dependent and suffer from insufficient reactivity compared to other enzymatic tools, such as glucose dehydrogenase. An efficient and competitive NADP + -utilizing FDH necessitates the availability and robustness of NADPH regeneration systems. Herein, we report the engineering of a new FDH from Candida dubliniensis (CdFDH), which showed no strict NAD + preference by a structure-guided rational/semi-rational design. A combinatorial mutant CdFDH-M4 (D197Q/Y198R/Q199N/A372S/K371T/▵Q375/K167R/H16L/K159R) exhibited 75-fold intensification of catalytic efficiency (k cat /K m ). Moreover, CdFDH-M4 has been successfully employed in diverse asymmetric oxidative/reductive processes with cofactor total turnover numbers (TTNs) ranging from 135 to 986, making it potentially useful for NADPH-required biocatalytic transformations.

  • Organizational Affiliation

    State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase
A, B, C, D
386Candida dubliniensis CD36Mutation(s): 0 
Gene Names: Cd36_53500CD36_53500
Find proteins for B9WHT3 (Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841))
Explore B9WHT3 
Go to UniProtKB:  B9WHT3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9WHT3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.229 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.402α = 90
b = 60.156β = 90
c = 120.482γ = 111.02
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Database references