6AHC | pdb_00006ahc

Cryo-EM structure of aldehyde-alcohol dehydrogenase reveals a high-order helical architecture critical for its activity

• PDB DOI: https://doi.org/10.2210/pdb6AHC/pdb
• EM Map EMD-9623: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-17 Released: 2019-08-21 
• Deposition Author(s): Kim, G., Song, J.J.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity.

Kim, G., Azmi, L., Jang, S., Jung, T., Hebert, H., Roe, A.J., Byron, O., Song, J.J.

(2019) Nat Commun 10: 4527-4527

• PubMed: 31586059 
• DOI: https://doi.org/10.1038/s41467-019-12427-8
• Primary Citation Related Structures: 
  6AHC


• PubMed Abstract: 
  

  Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity.

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Organizational Affiliation: 
• Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.
Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83, Huddinge, Sweden.
School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A6B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 771.11 kDa 
• Atom Count: 46,106 
• Modeled Residue Count: 6,052 
• Deposited Residue Count: 7,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde-alcohol dehydrogenase	A, B, C, D, E, F, G, H	893	Escherichia coli K-12	Mutation(s): 0  EC: 1.1.1.1 (PDB Primary Data), 1.2.1.10 (PDB Primary Data)
UniProt
Find proteins for P0A9Q7 (Escherichia coli (strain K12)) Explore P0A9Q7  Go to UniProtKB:  P0A9Q7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.45 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Kim, G., Song, J.J.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2016K1A1A2912057
National Research Foundation (Korea)	Korea, Republic Of	NRF-2016R1A2B3006293

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references
• Version 1.3: 2025-07-02
  Changes: Data collection, Structure summary