9X0Q | pdb_00009x0q

Cryo-EM Structure of Alcohol Dehydrogenase Variant from Gluconobacter oxydans Truncating Membrane-Binding Regions (Form 1)

PDB DOI: https://doi.org/10.2210/pdb9X0Q/pdb
EM Map EMD-66439: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Gluconobacter oxydans
Expression System: Gluconobacter oxydans
Mutation(s): No

Deposited: 2025-09-30 Released: 2026-08-26
Deposition Author(s): Ichikawa, K., Adachi, T., Miyata, T., Makino, F., Namba, K., Kitazumi, Y., Shirai, O., Sowa, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure-guided engineering of membrane-binding regions for surfactant-free solubilization of direct electron transfer-type alcohol dehydrogenase.

Ichikawa, K., Adachi, T., Miyata, T., Makino, F., Namba, K., Kitazumi, Y., Shirai, O., Sowa, K.

(2026) Chem Commun (Camb) 62: 7948-7952

PubMed: 41853871 Search on PubMed
DOI: https://doi.org/10.1039/d6cc00143b
Primary Citation Related Structures:
9X0Q, 9X0R

PubMed Abstract:
Membrane-bound alcohol dehydrogenase (ADH) from Gluconobacter oxydans is a direct electron transfer-type biocatalyst for ethanol oxidation. To improve its bioelectrocatalysis, membrane-binding regions of ADH were predicted, resulting in the construction of a soluble ADH variant by enzyme engineering. The variant was purified and characterized using structural and bioelectrochemical approaches.

Organizational Affiliation

Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan. sowa.keisei.2u@kyoto-u.ac.jp.

Macromolecule Content

Total Structure Weight: 149.01 kDa
Atom Count: 9,535
Modeled Residue Count: 1,216
Deposited Residue Count: 1,352
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase (quinone), dehydrogenase subunit	A	757	Gluconobacter oxydans	Mutation(s): 0 Gene Names: adhA, GOX1068 EC: 1.1.5.5
UniProt
Find proteins for O05542 (Gluconobacter oxydans (strain 621H)) Explore O05542 Go to UniProtKB: O05542
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O05542
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase (quinone), cytochrome c subunit	B	462	Gluconobacter oxydans	Mutation(s): 0 Gene Names: adhB, GOX1067 EC: 1.1.5.5
UniProt
Find proteins for Q47945 (Gluconobacter oxydans (strain 621H)) Explore Q47945 Go to UniProtKB: Q47945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q47945
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small subunit of alcohol dehydrogenase	C	133	Gluconobacter oxydans	Mutation(s): 0 EC: 1.1.5.5
UniProt
Find proteins for O05544 (Gluconobacter oxydans (strain 621H)) Explore O05544 Go to UniProtKB: O05544
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O05544
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], G [auth B], H [auth B], I [auth B]	HEME C C₃₄ H₃₆ Fe N₄ O₄ YZTICFPLOXKSQO-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
PQQ (Subject of Investigation/LOI) Query on PQQ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PYRROLOQUINOLINE QUINONE C₁₄ H₆ N₂ O₈ MMXZSJMASHPLLR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.2.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP23K19281
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K14831
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121003