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- EMDB-48542: Electron bifurcating tungstopyranopterin-containing aldehyde oxid... -

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Basic information

Entry
Database: EMDB / ID: EMD-48542
TitleElectron bifurcating tungstopyranopterin-containing aldehyde oxidoreductase WorABCSL with NADH
Map data
Sample
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex WorABCSL
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit L
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit S
Keywordselectron bifurcation / OXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
: / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain ...: / Aldehyde ferredoxin oxidoreductase, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal / Aldehyde ferredoxin oxidoreductase, domain 2 / Aldehyde ferredoxin oxidoreductase, domain 3 / Aldehyde ferredoxin oxidoreductase-like, C-terminal / Aldehyde ferredoxin oxidoreductase, N-terminal domain superfamily / : / Aldehyde ferredoxin oxidoreductase, domains 2 & 3 / Aldehyde ferredoxin oxidoreductase, N-terminal domain / Aldehyde ferredoxin oxidoreductase, N-terminal domain / 4Fe-4S dicluster domain / 4Fe-4S binding domain / 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
Fe-S-cluster-containing hydrogenase subunit / Aldehyde:ferredoxin oxidoreductase
Similarity search - Component
Biological speciesAcetomicrobium mobile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFeng X / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136885 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: An electron-bifurcating "plug" to a protein nanowire in tungsten-dependent aldehyde detoxification.
Authors: Xiang Feng / Gerrit J Schut / Saisuki Putumbaka / Huilin Li / Michael W W Adams /
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 ...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 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.
History
DepositionJan 6, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48542.png

Downloads & links

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Map

FileDownload / File: emd_48542.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å		0.83 Å/pix.
x 360 pix.
= 298.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.1555526 - 2.0550618
Average (Standard dev.)0.00015354367 (±0.03506099)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48542_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_48542_half_map_2.map
Projections & Slices
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Sample components

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Entire : electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

EntireName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex WorABCSL
Components
  • Complex: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex WorABCSL
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit L
    • Protein or peptide: tungstopyranopterin-containing aldehyde oxidoreductase subunit S

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Supramolecule #1: electron-bifurcating tungstopyranopterin-containing aldehyde oxid...

SupramoleculeName: electron-bifurcating tungstopyranopterin-containing aldehyde oxidoreductase complex WorABCSL
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acetomicrobium mobile (bacteria)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: tungstopyranopterin-containing aldehyde oxidoreductase subunit L

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase subunit L
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString: MFGYMGKVLR VNLSTKNITL EPLRMDWAKD FLGARGLGSR YLVEEVDPNV DPFSPDNKLI FATGPVTGTL ATSAGRFNVV TKGPLTGTI AASNSGGYFG PELKYAGYDM IIFEGKSANP VYLWIYNDHV ELRDASHVWG KDSYETTDAL LSETDPEAKV A CIGPAGER ...String:
MFGYMGKVLR VNLSTKNITL EPLRMDWAKD FLGARGLGSR YLVEEVDPNV DPFSPDNKLI FATGPVTGTL ATSAGRFNVV TKGPLTGTI AASNSGGYFG PELKYAGYDM IIFEGKSANP VYLWIYNDHV ELRDASHVWG KDSYETTDAL LSETDPEAKV A CIGPAGER LVLFACVMND KHRAAGRTGV GAVMGSKNLK AVVVRGTGGI KLADKEAFLE ALRKARKKIA EHPVTGGGLP AY GTNVLVN VINAAGALPT RNFKEAWFEG ADKISGETMA ETILLKNKAC ASCASACGRV TKAMGEIGEG PEYEAVWAYG AQC GVDNLE AICKANFICN KLGMDPITMG STIGCAMELA ELGLIDEKKA GVSLHWGNAE AIVKLTEDTG YRRGFGEELA LGSY RLGEK YGHPELSMSA KKQEMPAYDP RALQGMGLEY ATSNRGGCHV RGYLTSPEVL GIPEKLDPTD IASKPQWTKT FQDLT AAVD SLGFCLFLTF ALDAGDLAAQ VAPIIGREVT AEELLLAGER IWNLERLFNL KAGISPKEDT LPPRLLNEPI PAGPSK GRV NKLHEMLPKY YELRGWGKNG IPTKERLESL GLLDIAAKYS L

UniProtKB: Aldehyde:ferredoxin oxidoreductase

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Macromolecule #2: tungstopyranopterin-containing aldehyde oxidoreductase subunit S

MacromoleculeName: tungstopyranopterin-containing aldehyde oxidoreductase subunit S
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Acetomicrobium mobile (bacteria)
SequenceString:
MEKVLVISPE KCVGCGSCEL ACSLEKEGEC RPSLARVTVY RFEAGANVPM TCQQCDDAPC ISVCKAGALA RDEKNVVQVD SSKCIGCRMC VMACPFGNMS YHWEQSTAIK CDQCNGSPYC VEFCPTKALD YVPADAISLQ KKKEFSARFA KIAQEVSE

UniProtKB: Fe-S-cluster-containing hydrogenase subunit

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMHEPES
300.0 mMSodium chlorideNaCl
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1042436
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 737246
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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