8RQZ | pdb_00008rqz

Crystal structure of Molybdenum bispyranopterin guanine dinucleotide formate dehydrogenases ForCE1 from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.231 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A scaffold for quinone channeling between membrane and soluble bacterial oxidoreductases.

Broc, M.Cherrier, M.V.Uzel, A.Arias-Cartin, R.Arnoux, P.Brasseur, G.Seduk, F.Guigliarelli, B.Legrand, P.Pierrel, F.Schoehn, G.Mate, M.J.Martin, L.Grimaldi, S.Nicolet, Y.Magalon, A.Walburger, A.

(2025) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-025-01607-4
  • Primary Citation of Related Structures:  
    8RQZ, 8RR0, 9GZQ

  • PubMed Abstract: 

    Redox processes are at the heart of energetic metabolism that drives life on earth. By extension, complex and efficient electron transfer wires are necessary to connect the various metabolic pathways that are often located in distinct cellular compartments. Here, we uncovered a structural module that enables channeling of quinones from the membrane to various water-soluble redox catalytic units in prokaryotes. Using X-ray crystallography and cryo-electron microscopy, we determined the structure of the unusual bacterial formate dehydrogenase ForCE that contains four ForC catalytic subunits docked around a membrane-associated tetrameric ForE central scaffold. In the latter, a conserved domain that we propose to name helical membrane plugin (HMP) was identified as essential to link formate oxidation, in Bacillus subtilis, to the aerobic respiratory chain. Our bioinformatic analysis indicates that this HMP is associated with different quinone-reducing oxidoreductases, highlighting its broad importance as a functional unit to wire electrons between a given catalytic redox center and the quinone pool.


  • Organizational Affiliation
    • Aix Marseille Univ, CNRS, LCB, IMM, IM2B, Marseille, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YjgD
A, B
186Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for O34681 (Bacillus subtilis (strain 168))
Explore O34681 
Go to UniProtKB:  O34681
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34681
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable oxidoreductase YjgC
C, D
985Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
EC: 1
UniProt
Find proteins for O34720 (Bacillus subtilis (strain 168))
Explore O34720 
Go to UniProtKB:  O34720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34720
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
Q [auth C],
QA [auth D],
R [auth C],
RA [auth D]
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
LHG
Query on LHG

Download Ideal Coordinates CCD File 
K [auth B],
X [auth C]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MQ7 (Subject of Investigation/LOI)
Query on MQ7

Download Ideal Coordinates CCD File 
T [auth C],
TA [auth D]
MENAQUINONE-7
C46 H64 O2
RAKQPZMEYJZGPI-LJWNYQGCSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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M [auth C]
MA [auth D]
N [auth C]
NA [auth D]
O [auth C]
M [auth C],
MA [auth D],
N [auth C],
NA [auth D],
O [auth C],
OA [auth D],
P [auth C],
PA [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
BA [auth C],
E [auth A],
F [auth A],
I [auth B],
J [auth B]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
L [auth C],
LA [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MLI
Query on MLI

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EA [auth C]
FA [auth C]
GA [auth C]
IA [auth D]
V [auth C]
EA [auth C],
FA [auth C],
GA [auth C],
IA [auth D],
V [auth C],
VA [auth D],
W [auth C],
Z [auth C],
ZA [auth D]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
4MO (Subject of Investigation/LOI)
Query on 4MO

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S [auth C],
SA [auth D]
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
GOL
Query on GOL

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CA [auth C]
DA [auth C]
G [auth A]
H [auth B]
JA [auth D]
CA [auth C],
DA [auth C],
G [auth A],
H [auth B],
JA [auth D],
WA [auth D],
XA [auth D],
YA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
AA [auth C],
HA [auth D],
KA [auth D],
Y [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
U [auth C],
UA [auth D]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AB [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.231 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.833α = 90
b = 210.5β = 90
c = 494.213γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-IDEX-02
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05-02
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)FranceANR-17-EURE-0003
Agence Nationale de la Recherche (ANR)FranceANR-22-CE44-0035-01
Centre National de la Recherche Scientifique (CNRS)FranceMICROBIOCO2
Agence Nationale de la Recherche (ANR)FranceANR 16-CE29-0010-01

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Database references
  • Version 1.2: 2025-09-03
    Changes: Database references