9KW8 | pdb_00009kw8

Polyether epoxide hydrolase MonBI-MonBII complex with product analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 
    0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.216 (Depositor) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 

  • 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.


  • Organizational Affiliation
    • Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.

Macromolecule Content 

  • Total Structure Weight: 134.78 kDa 
  • Atom Count: 8,452 
  • Modeled Residue Count: 1,082 
  • Deposited Residue Count: 1,208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MonBI,MonBII
A, B, C, D
302Streptomyces virginiaeMutation(s): 0 
Gene Names: monBImonBII
UniProt
Find proteins for Q846W7 (Streptomyces virginiae)
Explore Q846W7 
Go to UniProtKB:  Q846W7
Find proteins for Q846W8 (Streptomyces virginiae)
Explore Q846W8 
Go to UniProtKB:  Q846W8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ846W8Q846W7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L6P
(Subject of Investigation/LOI)

Query on A1L6P



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
[(2~{S},3~{R})-2-methyl-3-[(2~{S},5~{R})-2-methyl-5-[(2~{S})-2,5,5-trimethyloxolan-2-yl]oxolan-2-yl]-3-oxidanyl-propyl] hexanoate
C22 H40 O5
WEWKCWFBYOEHQB-ZUCBFVJTSA-N
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.92α = 90
b = 135.008β = 90
c = 144.516γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan19H04634
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan21H01754
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan22K19282

Revision History  (Full details and data files)

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