5UMY

Crystal structure of TnmS3 in complex with tiancimycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Resistance to Enediyne Antitumor Antibiotics by Sequestration.

Chang, C.Y.Yan, X.Crnovcic, I.Annaval, T.Chang, C.Nocek, B.Rudolf, J.D.Yang, D.Babnigg, G.Joachimiak, A.Phillips Jr., G.N.Shen, B.

(2018) Cell Chem Biol 25: 1075-1085.e4

  • DOI: https://doi.org/10.1016/j.chembiol.2018.05.012
  • Primary Citation of Related Structures:  
    5UMP, 5UMQ, 5UMW, 5UMX, 5UMY, 6BBX

  • PubMed Abstract: 

    The enediynes, microbial natural products with extraordinary cytotoxicities, have been translated into clinical drugs. Two self-resistance mechanisms are known in the enediyne producers-apoproteins for the nine-membered enediynes and self-sacrifice proteins for the ten-membered enediyne calicheamicin. Here we show that: (1) tnmS1, tnmS2, and tnmS3 encode tiancimycin (TNM) resistance in its producer Streptomyces sp. CB03234, (2) tnmS1, tnmS2, and tnmS3 homologs are found in all anthraquinone-fused enediyne producers, (3) TnmS1, TnmS2, and TnmS3 share a similar β barrel-like structure, bind TNMs with nanomolar K D values, and confer resistance by sequestration, and (4) TnmS1, TnmS2, and TnmS3 homologs are widespread in nature, including in the human microbiome. These findings unveil an unprecedented resistance mechanism for the enediynes. Mechanisms of self-resistance in producers serve as models to predict and combat future drug resistance in clinical settings. Enediyne-based chemotherapies should now consider the fact that the human microbiome harbors genes encoding enediyne resistance.


  • Organizational Affiliation

    Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyoxalase/bleomycin resisance protein/dioxygenase
A, B
140Streptomyces sp. CB03234Mutation(s): 0 
Gene Names: tnmS3
UniProt
Find proteins for A0A125SA29 (Streptomyces sp. (strain CB03234))
Explore A0A125SA29 
Go to UniProtKB:  A0A125SA29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125SA29
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TNN
Query on TNN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(1aS,11S,11aR,14Z,18R)-3,8,18-trihydroxy-11a-[(1R)-1-hydroxyethyl]-7-methoxy-11,11a-dihydro-4H-11,1a-hept[3]ene[1,5]diynonaphtho[2,3-h]oxireno[c]quinoline-4,9(10H)-dione
C27 H19 N O8
DJOMZYYFFHCVSQ-UBZKRVARSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TNN Binding MOAD:  5UMY Kd: 108 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.79α = 90
b = 67.87β = 90
c = 84.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.3: 2020-09-23
    Changes: Structure summary
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description