7Z5O

W-formate dehydrogenase from Desulfovibrio vulgaris - Dithionite reduced form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.119 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Spectroscopic and Structural Characterization of Reduced Desulfovibrio vulgaris Hildenborough W-FdhAB Reveals Stable Metal Coordination during Catalysis.

Oliveira, A.R.Mota, C.Klymanska, K.Biaso, F.Romao, M.J.Guigliarelli, B.Pereira, I.C.

(2022) ACS Chem Biol 17: 1901-1909

  • DOI: https://doi.org/10.1021/acschembio.2c00336
  • Primary Citation of Related Structures:  
    7Z5O

  • PubMed Abstract: 

    Metal-dependent formate dehydrogenases are important enzymes due to their activity of CO 2 reduction to formate. The tungsten-containing FdhAB formate dehydrogenase from Desulfovibrio vulgaris Hildenborough is a good example displaying high activity, simple composition, and a notable structural and catalytic robustness. Here, we report the first spectroscopic redox characterization of FdhAB metal centers by EPR. Titration with dithionite or formate leads to reduction of three [4Fe-4S] 1+ clusters, and full reduction requires Ti(III)-citrate. The redox potentials of the four [4Fe-4S] 1+ centers range between -250 and -530 mV. Two distinct W V signals were detected, W D V and W F V , which differ in only the g 2 -value. This difference can be explained by small variations in the twist angle of the two pyranopterins, as determined through DFT calculations of model compounds. The redox potential of W VI/V was determined to be -370 mV when reduced by dithionite and -340 mV when reduced by formate. The crystal structure of dithionite-reduced FdhAB was determined at high resolution (1.5 Å), revealing the same structural alterations as reported for the formate-reduced structure. These results corroborate a stable six-ligand W coordination in the catalytic intermediate W V state of FdhAB.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, alpha subunit, selenocysteine-containingA [auth AAA]1,009Nitratidesulfovibrio 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, beta subunit, putativeB [auth BBB]236Nitratidesulfovibrio 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
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA]
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
Query on SF4

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E [auth AAA],
S [auth BBB],
T [auth BBB],
U [auth BBB]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)
Query on W

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G [auth AAA]TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
PEG
Query on PEG

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Q [auth AAA]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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H [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
L [auth AAA]
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA],
M [auth AAA],
N [auth AAA],
P [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
O [auth AAA],
R [auth AAA]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.119 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.811α = 90
b = 124.15β = 90
c = 149.666γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
PHASERphasing

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

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 2.0: 2022-07-20
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2022-07-27
    Changes: Database references
  • Version 2.2: 2024-01-31
    Changes: Data collection, Refinement description