9IJF | pdb_00009ijf

Structure of ATP-dependent diazotase CmaA6

• PDB DOI: https://doi.org/10.2210/pdb9IJF/pdb

• Classification: LIGASE
• Organism(s): Kutzneria albida DSM 43870
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-22 Released: 2025-05-07 
• Deposition Author(s): Katsuyama, Y., Kawai, S., Ohnishi, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: in silico

Literature

Structural Basis for the Catalytic Mechanism of ATP-Dependent Diazotase CmaA6.

Kawai, S., Karasawa, M., Moriwaki, Y., Terada, T., Katsuyama, Y., Ohnishi, Y.

(2025) Angew Chem Int Ed Engl 64: e202505851-e202505851

• PubMed: 40275441 
• DOI: https://doi.org/10.1002/anie.202505851
• Primary Citation of Related Structures:  
  8ZTZ, 9IJF


• PubMed Abstract: 
  

  Although several diazotases have been recently reported, the details of the reaction mechanism are not yet understood. In this study, we investigated the mechanism of CmaA6, an ATP-dependent diazotase, which catalyzes the diazotization of 3-aminocoumaric acid using nitrous acid. X-ray crystallography and cryogenic electron microscopy-single particle analysis revealed CmaA6 structures in the substrate-free and AMP-binding states. Kinetic analysis suggested that CmaA6 catalyzes diazotization via a sequential reaction mechanism in which three substrates (nitrous acid, ATP, and 3-aminocoumaric acid) are simultaneously bound in the reaction pocket. The nitrous acid and 3-aminocoumaric acid binding sites were predicted based on the AMP-binding state and confirmed by site-directed mutagenesis. In addition, computational analysis revealed a tunnel for 3-aminocoumaric acid to enter the reaction pocket, which was advantageous for the sequential reaction mechanism. This study provides important insights into the catalytic mechanism of diazotization in natural product biosynthesis.

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Organizational Affiliation: 
• Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
Division of Computational Drug Discovery and Design, Medical Research Laboratory, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 496.31 kDa 
• Atom Count: 32,117 
• Modeled Residue Count: 4,198 
• Deposited Residue Count: 4,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative AMP-binding enzyme	A, B, C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I]	569	Kutzneria albida DSM 43870	Mutation(s): 0  Gene Names: KALB_2256
UniProt
Find proteins for W5W4E6 (Kutzneria albida DSM 43870) Explore W5W4E6  Go to UniProtKB:  W5W4E6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.163	α = 76.31
b = 101.068	β = 88.051
c = 157.411	γ = 62.283

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Katsuyama, Y., Kawai, S., Ohnishi, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H04645
Japan Society for the Promotion of Science (JSPS)	Japan	19H05685
Japan Society for the Promotion of Science (JSPS)	Japan	22H05130
Japan Society for the Promotion of Science (JSPS)	Japan	22KJ1046

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Database references