9BQ0

Complex structure of protein crystal of Tri17 with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.281 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enzymatic synthesis of azide by a promiscuous N-nitrosylase.

Del Rio Flores, A.Zhai, R.Kastner, D.W.Seshadri, K.Yang, S.De Matias, K.Shen, Y.Cai, W.Narayanamoorthy, M.Do, N.B.Xue, Z.Marzooqi, D.A.Kulik, H.J.Zhang, W.

(2024) Nat Chem 16: 2066-2075

  • DOI: https://doi.org/10.1038/s41557-024-01646-2
  • Primary Citation of Related Structures:  
    8TF7, 9BQ0

  • PubMed Abstract: 

    Azides are energy-rich compounds with diverse representation in a broad range of scientific disciplines, including material science, synthetic chemistry, pharmaceutical science and chemical biology. Despite ubiquitous usage of the azido group, the underlying biosynthetic pathways for its formation remain largely unknown. Here we report the characterization of an enzymatic route for de novo azide construction. We demonstrate that Tri17, a promiscuous ATP- and nitrite-dependent enzyme, catalyses organic azide synthesis through sequential N-nitrosation and dehydration of aryl hydrazines. Through biochemical, structural and computational analyses, we further propose a plausible molecular mechanism for azide synthesis that sets the stage for future biocatalytic applications and biosynthetic pathway engineering.


  • Organizational Affiliation

    Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMP-binding protein
A, B, C, D
564Streptomyces tsukubensisMutation(s): 0 
Gene Names: B7R87_11280EWI31_19020
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
L [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
I [auth B]
K [auth C]
M [auth D]
F [auth A],
H [auth B],
I [auth B],
K [auth C],
M [auth D],
N [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.281 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.095α = 90
b = 152.331β = 90
c = 229.642γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM136758

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references