9K2F | pdb_00009k2f

Crystal Structure of CyaF/SAH in open conformational state

• PDB DOI: https://doi.org/10.2210/pdb9K2F/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Actinoalloteichus caeruleus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-17 Released: 2025-10-22 
• Deposition Author(s): Chen, R.J., Zhang, L.P., Zhu, Y.G., Zhang, C.S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.278 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: in silico

Literature

Biochemical and Structural Insights of the N -Methyltransferase CyaF in Cyanogramide Biosynthesis.

Chen, R., Zhang, Q., Zhang, L., Fang, C., Zhu, H., Zhu, W., Zhang, C., Zhu, Y.

(2025) J Nat Prod 88: 715-722

• PubMed: 40053516 
• DOI: https://doi.org/10.1021/acs.jnatprod.4c01391
• Primary Citation Related Structures: 
  9K2F


• PubMed Abstract: 
  

  N -Methyltransferases involved in indole methylation have seldom been discovered in natural product biosynthesis. This study focuses on the enzyme CyaF, which catalyzes a critical N -methylation step of indole in the β-carboline skeleton during cyanogramide biosynthesis. Seven β-carboline analogues ( 3 - 9 ) were isolated from the recombinant strain Streptomyces coelicolor YF11/ cyaABC , including three new compounds ( 5 - 7 ). In vitro assays revealed CyaF's substrate flexibility. The crystal structure of the CyaF/ S -adenosyl-L-homocysteine (SAH) complex, combined with the AlphaFold-predicted model and site-directed mutagenesis, elucidated the catalytic mechanism and structural features that enable CyaF to accommodate diverse substrates, highlighting its potential for biocatalytic applications.

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Organizational Affiliation: 
• State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People's Republic of China.
University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.
Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572000, People's Republic of China.
Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 57.18 kDa 
• Atom Count: 3,501 
• Modeled Residue Count: 456 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CyaF	A [auth B], B [auth D]	262	Actinoalloteichus caeruleus	Mutation(s): 0
UniProt
Find proteins for A0A6M3FWK4 (Actinoalloteichus cyanogriseus) Explore A0A6M3FWK4  Go to UniProtKB:  A0A6M3FWK4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	C [auth B], D	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.278 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.355	α = 90
b = 103.045	β = 90
c = 122.381	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Chen, R.J., Zhang, L.P., Zhu, Y.G., Zhang, C.S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177119
National Natural Science Foundation of China (NSFC)	China	22193072

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Database references