9KW7 | pdb_00009kw7

Polyether epoxide hydrolase MonBI K7A mutant

• PDB DOI: https://doi.org/10.2210/pdb9KW7/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces virginiae
• Expression System: Escherichia
• Mutation(s): Yes 


• Deposited: 2024-12-05 Released: 2025-12-10 
• Deposition Author(s): Yao, M., Arai, A., Minami, A., Ozaki, T., Kumeta, H., Oikawa, H., Ose, T.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

A system of paired polyether epoxide hydrolases enables a mouldable enzyme for consecutive ring cyclization cascades.

Yabuno, N., Minami, A., Ozaki, T., Owada, Y., Sawada, K., Arai, A., Sato, S., Sugiyama, A., Tadokoro, T., Aizawa, T., Dosen, T., Nomai, T., Matsumaru, T., Liu, J., Ye, T., Kodama, A., Uchiyama, S., Hengphasatporn, K., Shigeta, Y., Saio, T., Maenaka, K., Yao, M., Kumeta, H., Oikawa, H., Ose, T.

(2026) Nat Chem 

• PubMed: 41992003 
• DOI: https://doi.org/10.1038/s41557-026-02122-9
• Primary Citation Related Structures: 
  9KW6, 9KW7, 9KW8


• PubMed Abstract: 
  

  Ionophore polyethers, a major class of polyketide-derived natural products, are characterized by molecular skeletons featuring arrays of tetrahydrofuran and tetrahydropyran rings. However, the precise mechanism underlying their biosynthesis, suggested to occur by a sequential epoxide-opening and ether cyclization cascade to generate more than two ether rings, remains elusive. Here we explore the biosynthesis of monensin and reveal the indispensability of a heterodimeric assembly of polyether epoxide hydrolases (MonBI·MonBII), with MonBII providing the sole active site. Structural analysis demonstrated that MonBII harbours an unusually large cavity, enabling the consecutive cyclization of substrates containing γ-hydroxy triepoxide moieties. This cavity is formed by the remarkable flexibility of MonBII, which undergoes a dramatic structural transition from a predominantly disordered state to its active folded conformation exclusively in the presence of MonBI. Given the widespread conservation of MonBI- and MonBII-type enzymes, this study emphasizes a unified pairing mechanism, wherein one protomer functions as a molecular mould, facilitating the folding process and stabilizing the structure of its partner for catalysis.

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Organizational Affiliation: 
• Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan. [e-mail].
Department of Chemistry, Institute of Science Tokyo, Tokyo, Japan. [e-mail].
Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.
Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Department of Chemistry, Institute of Science Tokyo, Tokyo, Japan.
School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, China.
Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea.
State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.
Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan.
Department of Biotechnology, Graduate School of Engineering, The University of Osaka, Osaka, Japan.
Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan.
Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan. [e-mail].
Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.05 kDa 
• Atom Count: 2,278 
• Modeled Residue Count: 284 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MonBI	A [auth B], B [auth A]	160	Streptomyces virginiae	Mutation(s): 1  Gene Names: monBI
UniProt
Find proteins for Q846W7 (Streptomyces virginiae) Explore Q846W7  Go to UniProtKB:  Q846W7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth B], D [auth B], E [auth B], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.981	α = 90
b = 135.981	β = 90
c = 66.175	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Yao, M., Arai, A., Minami, A., Ozaki, T., Kumeta, H., Oikawa, H., Ose, T.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	19H04634
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H01754
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	22K19282

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release
  
• Version 1.1: 2026-04-29
  Changes: Database references