7OWB | pdb_00007owb

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 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 41.26 kDa 
  • Atom Count: 2,594 
  • Modeled Residue Count: 333 
  • Deposited Residue Count: 370 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 A0ACD6BA77 (Streptomyces sp. ZEA17I)
Explore A0ACD6BA77 
Go to UniProtKB:  A0ACD6BA77
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BA77
Sequence Annotations
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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 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
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



Ligand Structure Quality Assessment 


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
  • Version 1.3: 2025-12-10
    Changes: Data collection, Structure summary