8ZLS | pdb_00008zls

Apo structure of BBE-like oxidative cyclase MaDS1

• PDB DOI: https://doi.org/10.2210/pdb8ZLS/pdb

• Classification: PLANT PROTEIN
• Organism(s): Morus alba
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-05-21 Released: 2025-08-13 
• Deposition Author(s): Guo, N., Fan, J., Yang, J., Lei, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Aspartic acid residues in BBE-like enzymes from Morus alba promote a function shift from oxidative cyclization to dehydrogenation.

Guo, N., Gu, J., Zhou, Q., Liu, F., Dong, H., Ding, Q., Wang, Q., Wu, D., Yang, J., Fan, J., Gao, L., Houk, K.N., Lei, X.

(2025) Proc Natl Acad Sci U S A 122: e2504346122-e2504346122

• PubMed: 40828030 
• DOI: https://doi.org/10.1073/pnas.2504346122
• Primary Citation Related Structures: 
  8ZLS, 8ZLT


• PubMed Abstract: 
  

  Berberine bridge enzyme (BBE)-like enzymes catalyze various oxidative cyclization and dehydrogenation reactions in natural product biosynthesis, but the molecular mechanism underlying the selectivity remains unknown. Here, we elucidated the catalytic mechanism of BBE-like oxidases from Morus alba involved in the oxidative cyclization and dehydrogenation of moracin C. X-ray crystal structures of a functionally promiscuous flavin adenine dinucleotide (FAD)-bound oxidase, MaDS1, with and without an oxidative dehydrogenation product were determined at 2.03 Å and 2.21 Å resolution, respectively. Structure-guided mutagenesis and sequence analysis have identified a conserved aspartic acid that directs the reaction toward the oxidative dehydrogenation pathway. A combination of density functional theory (DFT) calculations and molecular dynamics (MD) simulations has revealed that aspartic acid acts as the catalytic base to deprotonate the carbon-cation intermediate to generate the dehydrogenated product, which otherwise undergoes a spontaneous 6π electrocyclization in the oxidative cyclization pathway to furnish the 2H-benzopyran product.

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Organizational Affiliation: 
• Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569.
College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
Institute of Cancer Research, Shen Zhen Bay Laboratory, Shen Zhen 518132, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 119.42 kDa 
• Atom Count: 8,425 
• Modeled Residue Count: 999 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MaDS1	A, B	520	Morus alba	Mutation(s): 0
UniProt
Find proteins for A0A6C0TIW9 (Morus alba) Explore A0A6C0TIW9  Go to UniProtKB:  A0A6C0TIW9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.244	α = 90
b = 125.002	β = 95.848
c = 85.229	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Guo, N., Fan, J., Yang, J., Lei, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22193073

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Database references