4ZYJ

Streptomyces peucetius nitrososynthase dnmZ in TDP-bound state

  • Classification: OXIDOREDUCTASE
  • Organism(s): Streptomyces peucetius
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2015-05-21 Released: 2015-10-14 
  • Deposition Author(s): Sartor, L.M., Vey, J.L.
  • Funding Organization(s): CSU Program for Education and Research in Biotechnology, CSUN Office of Research and Sponsored Projects, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway.

Sartor, L.Ibarra, C.Al-Mestarihi, A.Bachmann, B.O.Vey, J.L.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1205-1214

  • DOI: https://doi.org/10.1107/S2053230X15014272
  • Primary Citation of Related Structures:  
    4ZXV, 4ZYJ

  • PubMed Abstract: 

    The anthracyclines are a class of highly effective natural product chemotherapeutics and are used to treat a range of cancers, including leukemia. The toxicity of the anthracyclines has stimulated efforts to further diversify the scaffold of the natural product, which has led to renewed interest in the biosynthetic pathway responsible for the formation and modification of this family of molecules. DnmZ is an N-hydroxylating flavin monooxygenase (a nitrososynthase) that catalyzes the oxidation of the exocyclic amine of the sugar nucleotide dTDP-L-epi-vancosamine to its nitroso form. Its specific role in the anthracycline biosynthetic pathway involves the synthesis of the seven-carbon acetal moiety attached to C4 of L-daunosamine observed in the anthracycline baumycin. Here, X-ray crystallography was used to elucidate the three-dimensional structure of DnmZ. Two crystal structures of DnmZ were yielded: that of the enzyme alone, solved to 3.00 Å resolution, and that of the enzyme in complex with thymidine diphosphate, the nucleotide carrier portion of the substrate, solved to 2.74 Å resolution. These models add insights into the structural features involved in substrate specificity and conformational changes involved in thymidine diphosphate binding by the nitrososynthases.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DnmZ
A, B, C, D
425Streptomyces peucetiusMutation(s): 0 
Gene Names: dnmZ
EC: 1.14.13.187 (PDB Primary Data), 1.14.13 (UniProt)
UniProt
Find proteins for A0A0R4I990 (Streptomyces peucetius)
Explore A0A0R4I990 
Go to UniProtKB:  A0A0R4I990
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R4I990
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.483α = 90
b = 134.667β = 90
c = 144.294γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CSU Program for Education and Research in BiotechnologyUnited States--
CSUN Office of Research and Sponsored ProjectsUnited States--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5SC2AI109500

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description