8RCA

W-formate dehydrogenase from Desulfovibrio vulgaris - Co-crystallized with Formate and Reoxidized by exposure to air for 1 h in the absence of Formate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement.

Vilela-Alves, G.Manuel, R.R.Viegas, A.Carpentier, P.Biaso, F.Guigliarelli, B.Pereira, I.A.C.Romao, M.J.Mota, C.

(2024) Chem Sci 15: 13090-13101

  • DOI: https://doi.org/10.1039/d4sc02394c
  • Primary Citation of Related Structures:  
    8RC8, 8RC9, 8RCA, 8RCB, 8RCC

  • PubMed Abstract: 

    Metal-dependent formate dehydrogenases are very promising targets for enzyme optimization and design of bio-inspired catalysts for CO 2 reduction, towards innovative strategies for climate change mitigation. For effective application of these enzymes, the catalytic mechanism must be better understood, and the molecular determinants clarified. Despite numerous studies, several doubts persist, namely regarding the role played by the possible dissociation of the SeCys ligand from the Mo/W active site. Additionally, the oxygen sensitivity of these enzymes must also be understood as it poses an important obstacle for biotechnological applications. This work presents a combined biochemical, spectroscopic, and structural characterization of Desulfovibrio vulgaris FdhAB ( Dv FdhAB) when exposed to oxygen in the presence of a substrate (formate or CO 2 ). This study reveals that O 2 inactivation is promoted by the presence of either substrate and involves forming a different species in the active site, captured in the crystal structures, where the SeCys ligand is displaced from tungsten coordination and replaced by a dioxygen or peroxide molecule. This form was reproducibly obtained and supports the conclusion that, although W- Dv FdhAB can catalyse the oxidation of formate in the presence of oxygen for some minutes, it gets irreversibly inactivated after prolonged O 2 exposure in the presence of either substrate.


  • Organizational Affiliation

    Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa 2829-516 Caparica Portugal cd.mota@fct.unl.pt mjr@fct.unl.pt.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, alpha subunit, selenocysteine-containing1,013Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: fdnG-1DVU_0587
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72EJ1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, beta subunit, putative214Nitratidesulfovibrio vulgaris str. HildenboroughMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72EJ0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
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)
Query on SF4

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B],
O [auth B],
P [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)
Query on W

Download Ideal Coordinates CCD File 
G [auth A]TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
M [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
F [auth A]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.558α = 90
b = 128.006β = 90
c = 148.905γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BII-BBF/2050/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04378/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/04378/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/04612/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04612/2020
Fundacao para a Ciencia e a TecnologiaPortugalLA/P/0140/2020
Fundacao para a Ciencia e a TecnologiaPortugalLA/P/0087/2020
Fundacao para a Ciencia e a TecnologiaPortugal2023.00286.BD

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Database references