8BQK

W-formate dehydrogenase from Desulfovibrio vulgaris - Soaking with Formate 22 min

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(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-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
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase, beta subunit, putative236Nitratidesulfovibrio 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 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
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E [auth A],
R [auth B],
S [auth B],
T [auth B]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
W (Subject of Investigation/LOI)
Query on W
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F [auth A]TUNGSTEN ION
W
FZFRVZDLZISPFJ-UHFFFAOYSA-N
PEG
Query on PEG
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N [auth A],
O [auth A]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL
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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],
M [auth A],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
P [auth A],
Q [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S
Download Ideal Coordinates CCD File 
G [auth A]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.684α = 90
b = 123.874β = 90
c = 149.181γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
STARANISOdata scaling
PHASERphasing
autoPROCdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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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 TecnologiaPortugalLA/P/0140/2020
Fundacao para a Ciencia e a TecnologiaPortugalLA/P/0087/2020

Revision History  (Full details and data files)

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