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- EMDB-75028: indoleacetate decarboxylase with bound indole-3-acetate -

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Basic information

Entry
Database: EMDB / ID: EMD-75028
Titleindoleacetate decarboxylase with bound indole-3-acetate
Map dataOuIAD tetramer map
Sample
  • Complex: homotetramer of indoleacetate decarboxylase with bound indole-3-acetate
    • Protein or peptide: Formate C-acetyltransferase
  • Ligand: 1H-INDOL-3-YLACETIC ACID
  • Ligand: water
Keywordsglycyl radical enzyme / decarboxylase / anaerobic / LYASE
Function / homology
Function and homology information


formate C-acetyltransferase / formate C-acetyltransferase activity / cytosol
Similarity search - Function
: / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain profile. / Glycine radical domain
Similarity search - Domain/homology
Formate C-acetyltransferase
Similarity search - Component
Biological speciesOlsenella uli DSM 7084 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsImrich CN / Drennan CL
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126982 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: The structural basis of malodorant skatole formation by the glycyl radical enzyme indoleacetate decarboxylase.
Authors: Christa N Imrich / Lindsey R F Backman / Abigail P Allworth / Mary C Andorfer / Jared C Paris / Nina M Greeley / Beverly Fu / Emily P Balskus / Catherine L Drennan /
Abstract: Glycyl radical enzymes (GREs) catalyze challenging chemical reactions using a posttranslationally installed glycyl radical cofactor. One such enzyme, indoleacetate decarboxylase (IAD), performs the ...Glycyl radical enzymes (GREs) catalyze challenging chemical reactions using a posttranslationally installed glycyl radical cofactor. One such enzyme, indoleacetate decarboxylase (IAD), performs the radical-based decarboxylation of indole-3-acetate (I3A) to form the malodorant molecule skatole. In addition to being an odor nuisance, skatole is a human and livestock lung toxin, a suspected carcinogen, and a mosquito attractant, all of which impact human health, agriculture, food production, and wastewater treatment. Here, we use cryogenic electron microscopy to solve a 2.45-Å resolution structure of IAD from the gut bacterium . We observe IAD in a homotetrameric form with the substrate I3A bound in all four protomers. The positioning of I3A in the active site is unexpected and is more consistent with a Kolbe-type decarboxylation mechanism, i.e., a decarboxylation initiated by a 1-electron oxidation of the carboxylate moiety rather than being initiated by hydrogen atom transfer (HAT). Previously, a high deuterium content in skatole from IAD assays in DO was used to support a HAT mechanism over a Kolbe-type mechanism. However, we show here that deuterium content does not necessarily inform on mechanism as IAD can catalyze the exchange of skatole's 3'-methyl hydrogens postturnover. Structural comparisons show that both IAD and hydroxyphenylacetate decarboxylase display structural features that are not found in other characterized GREs, suggesting that they represent a distinct GRE-subclass. Collectively, these insights will inform IAD inhibitor design aimed at decreasing skatole production.
History
DepositionJan 8, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75028.png

Downloads & links

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Map

FileDownload / File: emd_75028.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOuIAD tetramer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00487
Minimum - Maximum-0.019097567 - 0.044581167
Average (Standard dev.)0.00011578484 (±0.0013867742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2

Fileemd_75028_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_75028_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homotetramer of indoleacetate decarboxylase with bound indole-3-a...

EntireName: homotetramer of indoleacetate decarboxylase with bound indole-3-acetate
Components
  • Complex: homotetramer of indoleacetate decarboxylase with bound indole-3-acetate
    • Protein or peptide: Formate C-acetyltransferase
  • Ligand: 1H-INDOL-3-YLACETIC ACID
  • Ligand: water

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Supramolecule #1: homotetramer of indoleacetate decarboxylase with bound indole-3-a...

SupramoleculeName: homotetramer of indoleacetate decarboxylase with bound indole-3-acetate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Olsenella uli DSM 7084 (bacteria)
Molecular weightTheoretical: 101 KDa

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Macromolecule #1: Formate C-acetyltransferase

MacromoleculeName: Formate C-acetyltransferase / type: protein_or_peptide / ID: 1 / Details: 6xHis-thrombin cleavage site-IAD / Number of copies: 4 / Enantiomer: LEVO / EC number: formate C-acetyltransferase
Source (natural)Organism: Olsenella uli DSM 7084 (bacteria)
Molecular weightTheoretical: 101.384719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MEESLVLEML QTGKTATWPA KNQLQESGEV VDKEVKGTPS TDRTRRMKER FMNAKCKMDM EAPIAYTKA WREHEGKPLY VRRGLAYKYM LEHLTPAIRE DELITMSKTR YDRGATQVPQ FATDFMISFL TQAEDQKEEA K LYSVEGKD ...String:
MGSSHHHHHH SSGLVPRGSH MEESLVLEML QTGKTATWPA KNQLQESGEV VDKEVKGTPS TDRTRRMKER FMNAKCKMDM EAPIAYTKA WREHEGKPLY VRRGLAYKYM LEHLTPAIRE DELITMSKTR YDRGATQVPQ FATDFMISFL TQAEDQKEEA K LYSVEGKD EAHTVEEEGW TKVGQLFSIR EEEVKPMLEV LEYWKTRCVE NVSDDWMKTS FPYYQDYVNA KKVGLFPGSG LH AGCDGRW IPAYDVALGG LNRVIEECRE KIEKTVVTTK EVADKVFFWQ GCIYACEGAI AWAHNYAVEA RRLAETAVEP RKT ELLEMA ERLDRVPAEA PRNFMEAVQA LWTTQILVIS DSLALGVSPG RWGKFLEPYY EKDLAEGRIT KGQALEVMEL LRIK FSTEE YITPSLWAAM ASSNSFMNLA VGGLDPKTGK CTDNEIEDLI LEAGINMPTP QPTLSILLSD KTTDHLAIKA AECTK AGNG YPAWFNYDMM VQHNLAMYRD EGITLEDARN CALSGCVENG LAGTGHPIAH PAFYNEGKTI ELACNEGVDP RTGIKV MDG IVPIKTYEDL WDNFIKIREH FMHVYMQYWN EVVACQRDIH PKIMGSVLMH DCIESGRPVD NLGCRYNGSV TLLDSGT VN VVNGLAAIKK LVFEDHKYTW DEFKEAMDNN FGFVLGAEKG NFSMLNQEID PEKHMKYAHI HRDVLNAPKF GNDDDFVD D IFVDLWHDYD RVTASETTYN GYRWITAALS ISAHGPHGRV TGATPDGRLS GVTLCDGILS ASPGTDVNGP IALIRSGVK LDPTEFASVQ LNMKFHPTAI RGDEGSRNFV DFIHSYFQMG GYHVQFNIVD SKMLRDAQDH PQNYRDLMVR VAGFSAYWNE LGKPIQDEV IARTEYDAL

UniProtKB: Formate C-acetyltransferase

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Macromolecule #2: 1H-INDOL-3-YLACETIC ACID

MacromoleculeName: 1H-INDOL-3-YLACETIC ACID / type: ligand / ID: 2 / Number of copies: 4 / Formula: IAC
Molecular weightTheoretical: 175.184 Da
Chemical component information

ChemComp-IAC:
1H-INDOL-3-YLACETIC ACID

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 685 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClsodium chloride
50.0 mMC8H18N2O4SHEPES
1.0 mMC10H9NO2Indole-3-acetic acid
0.1 % v/vC2H6OSdimethylsulfoxide
GridModel: Quantifoil Active R1.2/0.8 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 240 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 81 % / Chamber temperature: 297.35 K / Instrument: SPT LABTECH CHAMELEON / Details: plunge time 155 ms.
Detailsisolated dimer by gel filtration chromatography

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8927 / Average exposure time: 1.9 sec. / Average electron dose: 52.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2743992
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold2 model of IAD from Olsenalla uli
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 330270
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Residue range: 1-878 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-10al:
indoleacetate decarboxylase with bound indole-3-acetate

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