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- PDB-9gzq: Structure of ForCE lacking the Helical Membrane Plug-in (HMP; DUF1641) -

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Basic information

Entry
Database: PDB / ID: 9gzq
TitleStructure of ForCE lacking the Helical Membrane Plug-in (HMP; DUF1641)
Components
  • ForE1
  • Probable oxidoreductase YjgC
KeywordsELECTRON TRANSPORT / Formate dehydrogenase / DUF1641
Function / homology
Function and homology information


formate metabolic process / formate dehydrogenase (NAD+) activity / Oxidoreductases / molybdopterin cofactor binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / membrane
Similarity search - Function
Protein of unknown function DUF1641 / Protein of unknown function (DUF1641) / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region ...Protein of unknown function DUF1641 / Protein of unknown function (DUF1641) / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
MOLYBDENUM(IV) ION / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / IRON/SULFUR CLUSTER / Uncharacterized protein YjgD / Probable oxidoreductase YjgC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.626 Å
AuthorsArnoux, P. / Cherrier, M.V. / Nicolet, Y. / Legrand, P. / Broc, M. / Seduk, F. / Arias-Cartin, R. / Magalon, A. / Walburger, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0035-01 France
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: A scaffold for quinone channeling between membrane and soluble bacterial oxidoreductases.
Authors: M Broc / M V Cherrier / A Uzel / R Arias-Cartin / P Arnoux / G Brasseur / F Seduk / B Guigliarelli / P Legrand / F Pierrel / G Schoehn / M J Maté / L Martin / S Grimaldi / Y Nicolet / A Magalon / A Walburger /
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 ...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.
History
DepositionOct 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable oxidoreductase YjgC
B: ForE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,30510
Polymers133,1452
Non-polymers3,1598
Water00
1
A: Probable oxidoreductase YjgC
B: ForE1
hetero molecules

A: Probable oxidoreductase YjgC
B: ForE1
hetero molecules

A: Probable oxidoreductase YjgC
B: ForE1
hetero molecules

A: Probable oxidoreductase YjgC
B: ForE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)545,21840
Polymers532,5808
Non-polymers12,63832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area44000 Å2
ΔGint-758 kcal/mol
Surface area149680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.909, 215.909, 215.528
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Probable oxidoreductase YjgC


Mass: 111836.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yjgC, BSU12160 / Production host: Escherichia coli (E. coli) / References: UniProt: O34720, Oxidoreductases
#2: Protein ForE1


Mass: 21308.650 Da / Num. of mol.: 1 / Mutation: G111Stop
Source method: isolated from a genetically manipulated source
Details: A mutation (Gly111Stop) that lead to the absence of the HMP domain (DUF1641) on ForE1 subunit
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yjgD, BSU12170 / Production host: Escherichia coli (E. coli) / References: UniProt: O34681

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-4MO / MOLYBDENUM(IV) ION


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.72 Å3/Da / Density % sol: 73.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18M tri-Ammonium citrate, 2.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.73404 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73404 Å / Relative weight: 1
ReflectionResolution: 3.626→152.7 Å / Num. obs: 54862 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.99 / Net I/σ(I): 6.3
Reflection shellResolution: 3.63→3.72 Å / Rmerge(I) obs: 0.159 / Num. unique obs: 4099 / CC1/2: 0.35

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.626→44.06 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.617
RfactorNum. reflection% reflectionSelection details
Rfree0.3195 1524 -RANDOM
Rwork0.28 ---
obs0.2821 29022 99.6 %-
Displacement parametersBiso mean: 158.95 Å2
Baniso -1Baniso -2Baniso -3
1-37.6066 Å20 Å20 Å2
2--37.6066 Å20 Å2
3----75.2132 Å2
Refine analyzeLuzzati coordinate error obs: 0.73 Å
Refinement stepCycle: LAST / Resolution: 3.626→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8501 0 131 0 8632
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078824HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9111988HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3136SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1539HARMONIC5
X-RAY DIFFRACTIONt_it8668HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1153SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7564SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion21.03
LS refinement shellResolution: 3.63→3.65 Å
RfactorNum. reflection% reflection
Rfree0.5884 37 -
Rwork0.4445 --
obs0.4529 581 93.47 %

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