7WUW

Crystal structure of AziU3/U2 from Streptomyces sahachiroi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination.

Kurosawa, S.Hasebe, F.Okamura, H.Yoshida, A.Matsuda, K.Sone, Y.Tomita, T.Shinada, T.Takikawa, H.Kuzuyama, T.Kosono, S.Nishiyama, M.

(2022) J Am Chem Soc 144: 16164-16170

  • DOI: https://doi.org/10.1021/jacs.2c07243
  • Primary Citation of Related Structures:  
    7WUW, 7WUX

  • PubMed Abstract: 

    Natural products containing an aziridine ring, such as mitomycin C and azinomycin B, exhibit antitumor activities by alkylating DNA via their aziridine rings; however, the biosynthetic mechanisms underlying the formation of these rings have not yet been elucidated. We herein investigated the biosynthesis of vazabitide A, the structure of which is similar to that of azinomycin B, and demonstrated that Vzb10/11, with no similarities to known enzymes, catalyzed the formation of the aziridine ring via sulfate elimination. To elucidate the detailed reaction mechanism, crystallization of Vzb10/11 and the homologous enzyme, AziU3/U2, in the biosynthesis of azinomycin B was attempted, and the structure of AziU3/U2, which had a new protein fold overall, was successfully determined. The structural analysis revealed that these enzymes adjusted the dihedral angle between the amino group and the adjacent sulfate group of the substrate to almost 180° and enhanced the nucleophilicity of the C6-amino group temporarily, facilitating the S N 2-like reaction to form the aziridine ring. The present study reports for the first time the molecular basis for aziridine ring formation.


  • Organizational Affiliation

    Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AziU2
A, B
233Streptomyces sahachiroiMutation(s): 0 
UniProt
Find proteins for B4XYC0 (Streptomyces sahachiroi)
Explore B4XYC0 
Go to UniProtKB:  B4XYC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4XYC0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AziU3
C, D
352Streptomyces sahachiroiMutation(s): 0 
UniProt
Find proteins for B4XYC1 (Streptomyces sahachiroi)
Explore B4XYC1 
Go to UniProtKB:  B4XYC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4XYC1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.851α = 90
b = 132.203β = 90
c = 157.015γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan24228001
Japan Society for the Promotion of Science (JSPS)Japan17H06168
Japan Science and TechnologyJapanJPMJSP2108

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Database references