8YSB | pdb_00008ysb

Crystal structure of DynA1, a putative monoxygenase from Mivromonospora chersina.

• PDB DOI: https://doi.org/10.2210/pdb8YSB/pdb

• Classification: ISOMERASE
• Organism(s): Micromonospora chersina
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-03-22 Released: 2024-09-04 
• Deposition Author(s): Yan, X.F., Huang, H.W., Gao, Y.G., Liang, Z.X.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.289 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.266 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Starting Model: in silico

Literature

An Enzymatic Oxidation Cascade Converts delta-Thiolactone Anthracene to Anthraquinone in the Biosynthesis of Anthraquinone-Fused Enediynes.

Ma, G.L., Liu, W.Q., Huang, H., Yan, X.F., Shen, W., Visitsatthawong, S., Prakinee, K., Tran, H., Fan, X., Gao, Y.G., Chaiyen, P., Li, J., Liang, Z.X.

(2024) JACS Au 4: 2925-2935

• PubMed: 39211597 
• DOI: https://doi.org/10.1021/jacsau.4c00279
• Primary Citation Related Structures: 
  8YSB


• PubMed Abstract: 
  

  Anthraquinone-fused enediynes are anticancer natural products featuring a DNA-intercalating anthraquinone moiety. Despite recent insights into anthraquinone-fused enediyne (AQE) biosynthesis, the enzymatic steps involved in anthraquinone biogenesis remain to be elucidated. Through a combination of in vitro and in vivo studies, we demonstrated that a two-enzyme system, composed of a flavin adenine dinucleotide (FAD)-dependent monooxygenase (DynE13) and a cofactor-free enzyme (DynA1), catalyzes the final steps of anthraquinone formation by converting δ-thiolactone anthracene to hydroxyanthraquinone. We showed that the three oxygen atoms in the hydroxyanthraquinone originate from molecular oxygen (O ₂ ), with the sulfur atom eliminated as H ₂ S. We further identified the key catalytic residues of DynE13 and A1 by structural and site-directed mutagenesis studies. Our data support a catalytic mechanism wherein DynE13 installs two oxygen atoms with concurrent desulfurization and decarboxylation, whereas DynA1 acts as a cofactor-free monooxygenase, installing the final oxygen atom in the hydroxyanthraquinone. These findings establish the indispensable roles of DynE13 and DynA1 in AQE biosynthesis and unveil novel enzymatic strategies for anthraquinone formation.

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Organizational Affiliation: 
• School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China.
School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.
School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong 21210, Thailand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.71 kDa 
• Atom Count: 835 
• Modeled Residue Count: 110 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted ester cyclase	A	146	Micromonospora chersina	Mutation(s): 1  Gene Names: GA0070603_4190
UniProt
Find proteins for B2BM50 (Micromonospora chersina) Explore B2BM50  Go to UniProtKB:  B2BM50

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.289 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.266 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.976	α = 90
b = 84.16	β = 90
c = 83.228	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Yan, X.F., Huang, H.W., Gao, Y.G., Liang, Z.X.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	MOE2019-T2-2-099
Ministry of Education (MoE, Singapore)	Singapore	RG108/20

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2024-09-11
  Changes: Database references