9L4Q | pdb_00009l4q

Crystal structure of the carbamoyl N-methyltransferase Asc-Orf2 complexed with SAH

• PDB DOI: https://doi.org/10.2210/pdb9L4Q/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Amycolatopsis alba DSM 44262
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-20 Released: 2025-10-29 
• Deposition Author(s): Li, Z.Y., Zhu, D.Y., Shen, Y.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

A Carbamoyl N -Methyltransferase Catalyzes N -Methylation of the Primary Amide in Ansacarbamitocin Biosynthesis.

Li, Z., Yang, W., Sun, Z., Wang, H., Lu, C., Zhu, D., Shen, Y.

(2025) J Am Chem Soc 147: 24186-24192

• PubMed: 40601550 
• DOI: https://doi.org/10.1021/jacs.5c05398
• Primary Citation of Related Structures:  
  9L4Q


• PubMed Abstract: 
  

  Primary amide-specific N -methyltransferases are extremely scarce in microbial secondary metabolism. Here, Asc-Orf2, an N -methyltransferase involved in the biosynthesis of ansacarbamitocins, was identified to catalyze the methylation of the 3- O -carbamoyl moiety. Structural analysis identified an unprecedented NPPH catalytic motif, offering a mechanistic basis to overcome the chemical inertness of primary amides. The 3- O -( N -methyl)-carbamoyl maytansinoid derivatives, modified via Asc-Orf2-catalyzed methylation, exhibited markedly enhanced antitumor activity, highlighting the magic methylation effect in bioactivity modulation. Furthermore, structure-targeted engineering expanded the catalytic scope of Asc-Orf2, enabling the directed synthesis of an N -allylated carbamoyl maytansinoid derivative optimized for antibody-drug conjugate payload.

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Organizational Affiliation: 
• Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences (CAS), Qingdao 266071, China.
State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
School of Basic Medical Sciences, Shandong University, Jinan 250012, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.36 kDa 
• Atom Count: 3,459 
• Modeled Residue Count: 427 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase small domain-containing protein	A, B	214	Amycolatopsis alba DSM 44262	Mutation(s): 0  Gene Names: CFP75_27000
UniProt
Find proteins for A0A229RJG8 (Amycolatopsis alba DSM 44262) Explore A0A229RJG8  Go to UniProtKB:  A0A229RJG8

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.280 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.677	α = 89.65
b = 45.761	β = 89.83
c = 48.116	γ = 88.42

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Li, Z.Y., Zhu, D.Y., Shen, Y.M.

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

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release