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- EMDB-67739: Alcohol Oxidase Mod1p from Ogataea methanolica -

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Basic information

Entry
Database: EMDB / ID: EMD-67739
TitleAlcohol Oxidase Mod1p from Ogataea methanolica
Map datafull
Sample
  • Complex: Mod1p octamer in complex with a-FAD
    • Protein or peptide: alcohol oxidase
  • Ligand: ARABINO-FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: water
KeywordsALCOHOL OXIDASE / OXIDOREDUCTASE MODIFIED FAD (A-FAD) / Mod1p / OXIDOREDUCTASE
Function / homology
Function and homology information


methane catabolic process / alcohol oxidase activity / alcohol oxidase / methanol metabolic process / peroxisomal matrix / flavin adenine dinucleotide binding
Similarity search - Function
GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesOgataea methanolica (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.94 Å
AuthorsCai H-L / Shimada A / Hamaguchi T / Mizoguchi A / Yonekura K / Shimada M / Ebihara A / Tani K / Nakagawa T
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121004 Japan
CitationJournal: Microb Biotechnol / Year: 2026
Title: Cryo-EM Structures of Alcohol Oxidase Isozymes Reveal Structural Determinants of Cofactor Variation and Enzymatic Activity in Ogataea methanolica.
Authors: Hao-Liang Cai / Atsuhiro Shimada / Tasuku Hamaguchi / Akira Mizoguchi / Koji Yonekura / Kyohei Tsuchiyama / Masaya Shimada / Akio Ebihara / Kazutoshi Tani / Tomoyuki Nakagawa /
Abstract: Ogataea methanolica is a methylotrophic yeast that can produce diverse recombinant proteins using methanol as the sole carbon and energy source. Unlike most yeast species, which possess a single ...Ogataea methanolica is a methylotrophic yeast that can produce diverse recombinant proteins using methanol as the sole carbon and energy source. Unlike most yeast species, which possess a single alcohol oxidase, O. methanolica encodes two isoenzymes, Mod1p and Mod2p. This study examines the structural and functional differences between Mod1p and Mod2p homooctamers. Both enzymes were purified from MOD-disrupted strains and analysed using cryogenic electron microscopy, achieving resolutions of 1.9 and 2.7 Å for Mod1p and Mod2p, respectively. The two isozymes assemble as tetramers of dimers stabilized by extensive intersubunit interactions, largely mediated by protruding loop regions and C-terminal extensions. Despite overall structural similarities, Mod1p and Mod2p exhibit subtle differences in surface charge distribution and sequence composition within the FAD-binding domain. These variations correlate with distinct cofactor preferences, with Mod1p binding arabityl FAD and Mod2p binding canonical FAD. Thin-section electron microscopy further revealed that Mod1p and Mod2p form both homomeric and hybrid octamers that assemble into peroxisomal crystalloids essential for methanol metabolism. Collectively, our findings provide mechanistic insight into alcohol oxidase diversity in methylotrophic yeasts, advancing our understanding of methanol utilization and its applications in biotechnology.
History
DepositionDec 15, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67739.png

Downloads & links

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Map

FileDownload / File: emd_67739.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.2 Å		0.82 Å/pix.
x 400 pix.
= 329.2 Å		0.82 Å/pix.
x 400 pix.
= 329.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.081739046 - 0.24119967
Average (Standard dev.)0.00010199525 (±0.0068222363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: odd

Fileemd_67739_half_map_1.map
Annotationodd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even

Fileemd_67739_half_map_2.map
Annotationeven
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mod1p octamer in complex with a-FAD

EntireName: Mod1p octamer in complex with a-FAD
Components
  • Complex: Mod1p octamer in complex with a-FAD
    • Protein or peptide: alcohol oxidase
  • Ligand: ARABINO-FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Mod1p octamer in complex with a-FAD

SupramoleculeName: Mod1p octamer in complex with a-FAD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ogataea methanolica (fungus)

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Macromolecule #1: alcohol oxidase

MacromoleculeName: alcohol oxidase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: alcohol oxidase
Source (natural)Organism: Ogataea methanolica (fungus)
Molecular weightTheoretical: 74.011133 KDa
SequenceString: MAIPDEFDII VVGGGSTGCA LAGRLGNLDE NVTVALIEGG ENNINNPWVY LPGVYPRNMR LDSKTATFYS SRPSPHLNGR RAIVPCANI LGGGSSINFL MYTRASASDY DDWESEGWTT DELLPLMKKI ETYQRPCNNR ELHGFDGPIK VSFGNYTYPN G QDFIRAAE ...String:
MAIPDEFDII VVGGGSTGCA LAGRLGNLDE NVTVALIEGG ENNINNPWVY LPGVYPRNMR LDSKTATFYS SRPSPHLNGR RAIVPCANI LGGGSSINFL MYTRASASDY DDWESEGWTT DELLPLMKKI ETYQRPCNNR ELHGFDGPIK VSFGNYTYPN G QDFIRAAE SQGIPFVDDA EDLKCSHGAE HWLKWINRDL GRRSDSAHAY IHPTMRNKQN LFLITSTKCE KIIIENGVAT GI KTVPMKP TGSPKTQVAR TFKARKQIIV SCGTISSPLV LQRSGIGSAH KLRQVGIKPV VDLPGVGMNF QDHYCFFTPY HVK PDTPSF DDFVRGDKAV QKSAFDQWYA NKDGPLTTNG IEAGVKIRPT EEELATADDE FRAAYDDYFG NKPDKPLMHY SLIS GFFGD HTKIPNGKYM CMFHFLEYPF SRGFVHVVSP NPYDAPDFDP GFMNDPRDMW PMVWSYKKSR ETARRMDCFA GEVTS HHPH YPYDSPARAA DMDLETTKAY AGPDHFTANL YHGSWTVPIE KPTPKNAAHV TSNQVEKHRD IEYTKEDDAA IEDYIR EHT ETTWHCLGTC SMAPREGSKV VPTGGVVDSR LNVYGVEKLK VADLSICPDN VGCNTYSTAL LIGEKASTLV AEDLGYS GD ALKMTVPNFK LGTYEEAGLA RF

UniProtKB: alcohol oxidase

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Macromolecule #2: ARABINO-FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: ARABINO-FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 8 / Formula: FAS
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAS:
ARABINO-FLAVIN-ADENINE DINUCLEOTIDE

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 4384 / 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

Concentration6.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.5 µm

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Image processing #1

Image processing ID1
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 66366
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 66366
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5hsa


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-21ju:
Alcohol Oxidase Mod1p from Ogataea methanolica

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