9LDK | pdb_00009ldk

The complex structure of Escherichia coli AdhE (compact conformation)

• PDB DOI: https://doi.org/10.2210/pdb9LDK/pdb
• EM Map EMD-63003: EMDB EMDataResource

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-06 Released: 2025-10-01 
• Deposition Author(s): Konno, N., Miyake, K., Nishino, S., Omae, K., Yanagisawa, H., Tsuru, S., Kikkawa, M., Furusawa, C., Iwasaki, W.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.79 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Repeatability of protein structural evolution following convergent gene fusions.

Konno, N., Miyake, K., Nishino, S., Omae, K., Yanagisawa, H., Tsuru, S., Nishimura, Y., Kikkawa, M., Furusawa, C., Iwasaki, W.

(2025) Nat Commun 16: 8278-8278

• PubMed: 40983608 
• DOI: https://doi.org/10.1038/s41467-025-63898-x
• Primary Citation of Related Structures:  
  9LDK, 9LDL


• PubMed Abstract: 
  

  Convergent evolution of proteins provides insights into repeatability of genetic adaptation. While local convergence of proteins at residue or domain level has been characterized, global structural convergence by inter-domain/molecular interactions remains largely unknown. Here we present structural convergent evolution on fusion enzymes of aldehyde dehydrogenases (ALDHs) and alcohol dehydrogenases (ADHs). We discover BdhE (bifunctional dehydrogenase E), an enzyme clade that emerged independently from the previously known AdhE family through distinct gene fusion events. AdhE and BdhE show shared enzymatic activities and non-overlapping phylogenetic distribution, suggesting common functions in different species. Cryo-electron microscopy reveals BdhEs form donut-like homotetramers, contrasting AdhE's helical homopolymers. Intriguingly, despite distinct quaternary structures and < 30% amino acid sequence identity, both enzymes forms resemble dimeric structure units by ALDH-ADH interactions via convergently elongated loop structures. These findings suggest convergent gene fusions recurrently led to substrate channeling evolution to enhance two-step reaction efficiency. Our study unveils structural convergence at inter-domain/molecular level, expanding our knowledges on patterns behind molecular evolution exploring protein structural universe.

---

Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. [e-mail].
Department of General Systems Studies, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
RIKEN Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
RIKEN Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 384.98 kDa 
• Atom Count: 19,646 
• Modeled Residue Count: 2,568 
• Deposited Residue Count: 3,564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional aldehyde-alcohol dehydrogenase AdhE	A, B, C, D [auth F]	891	Escherichia coli K-12	Mutation(s): 0  Gene Names: adhE, ana, b1241, JW1228 EC: 1.2.1.10 (PDB Primary Data), 1.1.1.1 (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: 2.79 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Konno, N., Miyake, K., Nishino, S., Omae, K., Yanagisawa, H., Tsuru, S., Kikkawa, M., Furusawa, C., Iwasaki, W.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22J20318
Japan Society for the Promotion of Science (JSPS)	Japan	24H00870
Japan Society for the Promotion of Science (JSPS)	Japan	21H05247
Japan Society for the Promotion of Science (JSPS)	Japan	21H05248
Japan Science and Technology	Japan	JPMJER1902
Japan Agency for Medical Research and Development (AMED)	Japan	JP24ama121002

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release
  
• Version 1.1: 2025-10-08
  Changes: Data collection, Database references
• Version 1.2: 2025-10-15
  Changes: Data collection