9M2Z | pdb_00009m2z

Crystal structure of an DUF3237 protein from Aspergillus

• PDB DOI: https://doi.org/10.2210/pdb9M2Z/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Aspergillus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-28 Released: 2025-04-09 
• Deposition Author(s): Li, C.P., Jiang, Q.Y., Yang, M.H.
• Funding Organization(s): Ministry of Education (MoE, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.198 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: in silico

Literature

Biosynthesis of gamma-Alkylidenebutenolide Derivatives Reveals an Atom-Deleting Lactone Ring Contraction by Dual-Enzyme Cascade.

Li, C., Fu, Y., Zhu, L., Jiang, Q., Gu, L., Zhao, Y., Yang, M., Kong, L.

(2025) J Am Chem Soc 147: 41210-41215

• PubMed: 41178754 
• DOI: https://doi.org/10.1021/jacs.5c13197
• Primary Citation Related Structures: 
  9M2Z


• PubMed Abstract: 
  

  Ring contraction represents a characteristic atom-level skeletal editing strategy in natural products. While this biosynthetic approach has garnered increasing attention, its role in modifying the lactone ring size remains underexplored. Here, we report a novel δ- to γ-lactone contraction during γ-alkylidenebutenolide biosynthesis in Aspergillus candidus . This dual-enzymatic cascade involves multifunctional oxidase PesD oxidizing a PKS-derived α-pyrone to a cyclic carbonate intermediate, followed by the DUF3237 enzyme PesF excising a molecule of CO ₂ to achieve ring contraction─an unprecedented function for this enzyme family. Computational, crystallographic, and site-directed mutagenesis studies reveal that PesF employs a noncanonical acid-base mechanism, with Glu99 serving as a key catalytic residue that fulfills an unusual dual role.

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Organizational Affiliation: 
• State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
Institute for Safflower Industry Research, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization (Ministry of Education), School of Pharmacy, Shihezi University, Shihezi 832002, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.75 kDa 
• Atom Count: 1,179 
• Modeled Residue Count: 145 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3237 protein	A	157	Aspergillus	Mutation(s): 0
UniProt
Find proteins for A0A1L9TCT0 (Aspergillus sydowii CBS 593.65) Explore A0A1L9TCT0  Go to UniProtKB:  A0A1L9TCT0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.198 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.1	α = 90
b = 70.52	β = 90
c = 88.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Li, C.P., Jiang, Q.Y., Yang, M.H.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, China)	China	B18056

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release
  
• Version 1.1: 2026-10-28
  Changes: Database references