9MQX | pdb_00009mqx

Electron-bifurcating Tungstopyranopterin-containing aldehyde oxidoreductase with NADH

  • Classification: OXIDOREDUCTASE
  • Organism(s): Acetomicrobium mobile
  • Mutation(s): No 

  • Deposited: 2025-01-06 Released: 2025-07-16 
  • Deposition Author(s): Feng, X., Li, H.
  • Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An electron-bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification.

Feng, X.Schut, G.J.Putumbaka, S.Li, H.Adams, M.W.W.

(2025) Proc Natl Acad Sci U S A 122: e2501900122-e2501900122

  • DOI: https://doi.org/10.1073/pnas.2501900122
  • Primary Citation of Related Structures:  
    9MQX

  • PubMed Abstract: 

    Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes oxidize aldehydes to the corresponding acids while reducing the redox protein ferredoxin. They have been structurally characterized mainly using WORs from hyperthermophilic archaea. The WORs of some bacteria contain three additional subunits of the BfuABC family and these chimeric WorABCSL enzymes catalyze an electron-bifurcating reaction in which aldehyde oxidation is coupled to the simultaneous reduction of ferredoxin and nicotinamide adenine dinucleotide. In human gut microbes, electron bifurcation by WorABSL is proposed to enable the detoxification of aldehydes generated from cooked foods and in the tungstocentric production of beneficial short chain fatty acids from lactate, potentially impacting health. Herein we present the high-resolution cryogenic electron microscopy (cryo-EM) structure of the WorABCSL purified from the bacterium Acetomicrobium mobile. The structure reveals a surprising 1:3 stoichiometry between WorABC and WorSL, with the WorSL units forming a nanowire-like architecture leading from three Tuco-containing catalytic sites in WorL via strings of multiple iron-sulfur clusters in WorS to a single bifurcating WorABC core. Our structure uncovers a distinct domain arrangement that links three Tuco-dependent aldehyde oxidation sites with the bifurcation process and potentially facilitates environmental aldehyde oxidation.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase chain G-like protein247Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BTZ0 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
Explore I4BTZ0 
Go to UniProtKB:  I4BTZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BTZ0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase, NADH-binding (51 kD) subunit622Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BTY9 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
Explore I4BTY9 
Go to UniProtKB:  I4BTY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BTY9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 24 kD subunit159Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BTY8 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
Explore I4BTY8 
Go to UniProtKB:  I4BTY8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BTY8
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde:ferredoxin oxidoreductase
D, F, H
604Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BTZ2 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
Explore I4BTZ2 
Go to UniProtKB:  I4BTZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BTZ2
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fe-S-cluster-containing hydrogenase subunit
E, G, I
152Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BTZ1 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
Explore I4BTZ1 
Go to UniProtKB:  I4BTZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BTZ1
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTE (Subject of Investigation/LOI)
Query on PTE

Download Ideal Coordinates CCD File 
EA [auth F],
MA [auth H],
W [auth D]
TUNGSTOPTERIN COFACTOR
C20 H22 Mg N10 O14 P2 S4 W
DYJJSYQWWQOQKE-MAAILCHMSA-F
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
P [auth B]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

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O [auth B]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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AA [auth E]
BA [auth E]
CA [auth E]
DA [auth F]
HA [auth G]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth F],
HA [auth G],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
KA [auth G],
LA [auth H],
N [auth B],
PA [auth I],
QA [auth I],
RA [auth I],
S [auth B],
SA [auth I],
T [auth B],
V [auth D],
Z [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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L [auth A],
Q [auth B],
U [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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M [auth A],
R [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
FA [auth F]
GA [auth F]
NA [auth H]
OA [auth H]
X [auth D]
FA [auth F],
GA [auth F],
NA [auth H],
OA [auth H],
X [auth D],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21
RECONSTRUCTIONcryoSPARC4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0020085
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136885
Department of Energy (DOE, United States)United StatesDE-FG02-95ER20175

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Data collection, Database references