8HTY

Candida boidinii Formate Dehydrogenase Crystal Structure at 1.4 Angstrom Resolution

PDB DOI: https://doi.org/10.2210/pdb8HTY/pdb

Classification: OXIDOREDUCTASE
Organism(s): [Candida] boidinii
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-12-22 Released: 2023-01-18
Deposition Author(s): Gul, M., Yuksel, B., Bulut, H., DeMirci, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.190
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography.

Gul, M., Yuksel, B., Bulut, H., DeMirci, H.

(2023) Acta Crystallogr D Struct Biol 79: 1010-1017

PubMed: 37860962 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2059798323008070
Primary Citation of Related Structures:
8HTY, 8IQ7, 8IVJ

PubMed Abstract:
Candida boidinii NAD ⁺-dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential application in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of wild-type CbFDH at cryogenic and ambient temperatures, as well as that of the Val120Thr mutant at cryogenic temperature, determined at the Turkish Light Source `Turkish DeLight'. The structures reveal new hydrogen bonds between Thr120 and water molecules in the active site of the mutant CbFDH, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, these findings provide invaluable insights into future protein-engineering efforts that could potentially enhance the efficiency and effectiveness of CbFDH.

Organizational Affiliation

Department of Molecular Biology and Genetics, Koc University, 34450 Istanbul, Türkiye.

Macromolecule Content

Total Structure Weight: 162.8 kDa
Atom Count: 13,377
Modelled Residue Count: 1,419
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A, B, C, D	364	[Candida] boidinii	Mutation(s): 0 Gene Names: FDH
UniProt
Find proteins for A0A0A1EQY0 (Candida boidinii) Explore A0A0A1EQY0 Go to UniProtKB: A0A0A1EQY0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A1EQY0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D]