6CLW | pdb_00006clw

Crystal structure of TnmH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 
    0.254 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Characterization of TnmH as anO-Methyltransferase Revealing Insights into Tiancimycin Biosynthesis and Enabling a Biocatalytic Strategy To Prepare Antibody-Tiancimycin Conjugates.

Adhikari, A.Teijaro, C.N.Yan, X.Chang, C.Y.Gui, C.Liu, Y.C.Crnovcic, I.Yang, D.Annaval, T.Rader, C.Shen, B.

(2020) J Med Chem 63: 8432-8441

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00799
  • Primary Citation Related Structures: 
    6CLW, 6CLX

  • PubMed Abstract: 

    The enediynes are among the most cytotoxic molecules known, and their use as anticancer drugs has been successfully demonstrated by targeted delivery. Clinical advancement of the anthraquinone-fused enediynes has been hindered by their low titers and lack of functional groups to enable the preparation of antibody-drug conjugates (ADCs). Here we report biochemical and structural characterization of TnmH from the tiancimycin (TNM) biosynthetic pathway, revealing that (i) TnmH catalyzes regiospecific methylation at the C-7 hydroxyl group, (ii) TnmH exhibits broad substrate promiscuity toward hydroxyanthraquinones and S-alkylated SAM analogues and catalyzes efficient installation of reactive alkyl handles, (iii) the X-ray crystal structure of TnmH provides the molecular basis to account for its broad substrate promiscuity, and (iv) TnmH as a biocatalyst enables the development of novel conjugation strategies to prepare antibody-TNM conjugates. These findings should greatly facilitate the construction and evaluation of antibody-TNM conjugates as next-generation ADCs for targeted chemotherapy.

Macromolecule Content 

  • Total Structure Weight: 77.13 kDa 
  • Atom Count: 5,116 
  • Modeled Residue Count: 680 
  • Deposited Residue Count: 728 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
O-methyltransferase
A, B
364Streptomyces sp. CB03234Mutation(s): 0 
Gene Names: tnmHAMK26_31990
UniProt
Find proteins for A0A125SA05 (Streptomyces sp. (strain CB03234))
Explore A0A125SA05 
Go to UniProtKB:  A0A125SA05
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A125SA05
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.86α = 90
b = 110.86β = 90
c = 113.31γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2020-09-16
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description