ISDA: 8J3O

Deposition Date 2023-04-17

Release Date 2023-09-20

Last Version Date 2023-11-01

Entry Detail

PDB ID:

8J3O

Keywords:

OXIDOREDUCTASE

Title:

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

Biological Source:

Source Organism:

Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) (Taxon ID: 573826)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.65 Å

R-Value Free:

0.27

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Formate dehydrogenase
Gene (Uniprot):CD36_53500
Chain IDs:A, B, C, D
Chain Length:386
Number of Molecules:4
Biological Source:Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841)

UniProt ID:B9WHT3 Pfam ID:PF00389, PF02826

Ligand Molecules

NAI

Primary Citation

Engineering a Formate Dehydrogenase for NADPH Regeneration.

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

Chembiochem 24 e202300390 e202300390 (2023)

PMID: 37455264 DOI: 10.1002/cbic.202300390

Abstact

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 (kcat /Km). 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.

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Primary Citation of related structures