8CM7

W-formate dehydrogenase M405A from Desulfovibrio vulgaris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

An allosteric redox switch involved in oxygen protection in a CO 2 reductase.

Oliveira, A.R.Mota, C.Vilela-Alves, G.Manuel, R.R.Pedrosa, N.Fourmond, V.Klymanska, K.Leger, C.Guigliarelli, B.Romao, M.J.Cardoso Pereira, I.A.

(2024) Nat Chem Biol 20: 111-119

  • DOI: https://doi.org/10.1038/s41589-023-01484-2
  • Primary Citation of Related Structures:  
    8CM4, 8CM5, 8CM6, 8CM7

  • PubMed Abstract: 

    Metal-dependent formate dehydrogenases reduce CO 2 with high efficiency and selectivity, but are usually very oxygen sensitive. An exception is Desulfovibrio vulgaris W/Sec-FdhAB, which can be handled aerobically, but the basis for this oxygen tolerance was unknown. Here we show that FdhAB activity is controlled by a redox switch based on an allosteric disulfide bond. When this bond is closed, the enzyme is in an oxygen-tolerant resting state presenting almost no catalytic activity and very low formate affinity. Opening this bond triggers large conformational changes that propagate to the active site, resulting in high activity and high formate affinity, but also higher oxygen sensitivity. We present the structure of activated FdhAB and show that activity loss is associated with partial loss of the metal sulfido ligand. The redox switch mechanism is reversible in vivo and prevents enzyme reduction by physiological formate levels, conferring a fitness advantage during O 2 exposure.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.


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): 1 
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 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, putative215Nitratidesulfovibrio 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 8 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],
S [auth B],
T [auth B],
U [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
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
O [auth A],
V [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
K [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A],
L [auth A],
N [auth A],
P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.874α = 90
b = 123.833β = 90
c = 149.891γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling
XSCALEdata scaling
pointlessdata scaling

Structure Validation

View Full Validation Report



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 TecnologiaPortugalSFRH/BD/116515/2016
Fundacao para a Ciencia e a TecnologiaPortugalCOVID/BD/151766/2021
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04378/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/04378/2020
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 TecnologiaPortugalUIDB/04612/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04612/2020

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references
  • Version 1.2: 2024-01-03
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Structure summary