7OWB

Chimeric carminomycin-4-O-methyltransferase (DnrK) with a region from 10-hydroxylase CalMB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evolution-inspired engineering of anthracycline methyltransferases.

Dinis, P.Tirkkonen, H.Wandi, B.N.Siitonen, V.Niemi, J.Grocholski, T.Metsa-Ketela, M.

(2023) PNAS Nexus 2: pgad009-pgad009

  • DOI: https://doi.org/10.1093/pnasnexus/pgad009
  • Primary Citation of Related Structures:  
    7OWB, 7OY1, 7PG7, 7PGA, 7PGJ, 7PHD, 7PHE, 7PHF

  • PubMed Abstract: 

    Streptomyces soil bacteria produce hundreds of anthracycline anticancer agents with a relatively conserved set of genes. This diversity depends on the rapid evolution of biosynthetic enzymes to acquire novel functionalities. Previous work has identified S -adenosyl-l-methionine-dependent methyltransferase-like proteins that catalyze 4-O-methylation, 10-decarboxylation, or 10-hydroxylation, with additional differences in substrate specificities. Here we focused on four protein regions to generate chimeric enzymes using sequences from four distinct subfamilies to elucidate their influence in catalysis. Combined with structural studies we managed to depict factors that influence gain-of-hydroxylation, loss-of-methylation, and substrate selection. The engineering expanded the catalytic repertoire to include novel 9,10-elimination activity, and 4-O-methylation and 10-decarboxylation of unnatural substrates. The work provides an instructive account on how the rise of diversity of microbial natural products may occur through subtle changes in biosynthetic enzymes.


  • Organizational Affiliation

    Department of Life Technologies, University of Turku, BioCity, Tykistökatu 6, FIN-20014 Turku, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carminomycin 4-O-methyltransferase DnrK,Methyltransferase domain-containing protein370Streptomyces peucetiusStreptomyces sp. ZEA17IMutation(s): 0 
Gene Names: dnrKDKT74_09280
EC: 2.1.1.292
UniProt
Find proteins for Q06528 (Streptomyces peucetius)
Explore Q06528 
Go to UniProtKB:  Q06528
Find proteins for A0A2V2Q0Q4 (Streptomyces sp. ZEA17I)
Explore A0A2V2Q0Q4 
Go to UniProtKB:  A0A2V2Q0Q4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ06528A0A2V2Q0Q4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3VL (Subject of Investigation/LOI)
Query on 3VL

Download Ideal Coordinates CCD File 
B [auth A]methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate
C30 H35 N O10
LJZPVWKMAYDYAS-QKKPTTNWSA-N
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.8α = 90
b = 103.137β = 90
c = 66.485γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description