8BQI

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 3 min

• PDB DOI: https://doi.org/10.2210/pdb8BQI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Nitratidesulfovibrio vulgaris str. Hildenborough
• Mutation(s): No 


• Deposited: 2022-11-21 Released: 2023-01-18 
• Deposition Author(s): Vilela-Alves, G., Mota, C., Oliveira, A.R., Manuel, R.R., Pereira, I.C., Romao, M.J.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 

Starting Model: experimental

Literature

Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation.

Vilela-Alves, G., Manuel, R.R., Oliveira, A.R., Pereira, I.C., Romao, M.J., Mota, C.

(2022) Int J Mol Sci 24

• PubMed: 36613918 
• DOI: https://doi.org/10.3390/ijms24010476
• Primary Citation of Related Structures:  
  8BQG, 8BQH, 8BQI, 8BQJ, 8BQK, 8BQL


• PubMed Abstract: 
  

  Metal-dependent formate dehydrogenases (Fdh) catalyze the reversible conversion of CO ₂ to formate, with unrivalled efficiency and selectivity. However, the key catalytic aspects of these enzymes remain unknown, preventing us from fully benefiting from their capabilities in terms of biotechnological applications. Here, we report a time-resolved characterization by X-ray crystallography of the Desulfovibrio vulgaris Hildenborough SeCys/W-Fdh during formate oxidation. The results allowed us to model five different intermediate structures and to chronologically map the changes occurring during enzyme reduction. Formate molecules were assigned for the first time to populate the catalytic pocket of a Fdh. Finally, the redox reversibility of Dv FdhAB in crystals was confirmed by reduction and reoxidation structural studies.

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Organizational Affiliation: 

Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 142.67 kDa 
• Atom Count: 9,442 
• Modelled Residue Count: 1,177 
• Deposited Residue Count: 1,249 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, alpha subunit, selenocysteine-containing	A	1,013	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: fdnG-1 EC: 1.2.1.2
UniProt
Find proteins for Q72EJ1 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ1  Go to UniProtKB:  Q72EJ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, beta subunit, putative	B	236	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: DVU_0588
UniProt
Find proteins for Q72EJ0 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ0  Go to UniProtKB:  Q72EJ0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGD (Subject of Investigation/LOI)	C [auth A], D [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C20 H26 N10 O13 P2 S2 VQAGYJCYOLHZDH-ILXWUORBSA-N
SF4 (Subject of Investigation/LOI)	E [auth A], O [auth B], P [auth B], Q [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)	G [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N
PEG	H [auth A], K [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	L [auth A], M [auth A], N [auth A], R [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)	F [auth A]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15151/ESRF-ES-643877202

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.992	α = 90
b = 123.751	β = 90
c = 150.358	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
PHASER	phasing
autoPROC	data reduction
STARANISO	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Vilela-Alves, G., Mota, C., Oliveira, A.R., Manuel, R.R., Pereira, I.C., Romao, M.J.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BII-BBF/2050/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0140/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0087/2020

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary