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- PDB-21jv: Alcohol Oxidase Mod2p from Ogataea methanolica -

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Basic information

Entry
Database: PDB / ID: 21jv
TitleAlcohol Oxidase Mod2p from Ogataea methanolica
Componentsalcohol oxidase
KeywordsOXIDOREDUCTASE / ALCOHOL OXIDASE / OXIDOREDUCTASE CANONICAL FAD / Mod2p
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
FLAVIN-ADENINE DINUCLEOTIDE / alcohol oxidase
Similarity search - Component
Biological speciesOgataea methanolica (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsCai, H.-L. / Shimada, A. / Hamaguchi, T. / Mizoguchi, A. / Yonekura, K. / Shimada, M. / Ebihara, A. / Tani, K. / Nakagawa, T.
Funding support Japan, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alcohol oxidase
B: alcohol oxidase
C: alcohol oxidase
D: alcohol oxidase
E: alcohol oxidase
F: alcohol oxidase
G: alcohol oxidase
H: alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)596,13216
Polymers589,8478
Non-polymers6,2848
Water41,7052315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
alcohol oxidase


Mass: 73730.922 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Ogataea methanolica (fungus) / References: UniProt: Q9UVU1, alcohol oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2315 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mod2p octamer in complex with FAD / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ogataea methanolica (fungus)
Buffer solutionpH: 7
SpecimenConc.: 4.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3700 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 38.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing-ID
1EMAN2particle selection1
2SerialEMimage acquisition
4RELIONCTF correction1
7UCSF Chimeramodel fitting
9PHENIX1.20_4459model refinement
13RELION3D reconstruction1
14EMAN2particle selection2
19RELION3D reconstruction2
20EMAN2particle selection3
21RELIONCTF correction3
25RELION3D reconstruction3
Image processing
IDImage recording-ID
11
21
31
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING ONLY
22PHASE FLIPPING ONLY
33PHASE FLIPPING ONLY
Particle selection
IDImage processing-IDNum. of particles selected
11140102
22
33
3D reconstruction

Algorithm: FOURIER SPACE / Entry-ID: 21JV / Num. of particles: 17152 / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT

IDImage processing-ID
11
21
31
42
52
62
73
83
93
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 5HSA

5hsa


Accession code: 5HSA / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.65 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00243080
ELECTRON MICROSCOPYf_angle_d0.47858704
ELECTRON MICROSCOPYf_dihedral_angle_d10.31115944
ELECTRON MICROSCOPYf_chiral_restr0.0456200
ELECTRON MICROSCOPYf_plane_restr0.0047680

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