The crystal structure of urdamycin C-6 ketoreductase domain UrdMred with bound NADP and rabelomycin

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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Structure-based engineering of angucyclinone 6-ketoreductases.

Patrikainen, P.Niiranen, L.Thapa, K.Paananen, P.Tahtinen, P.Mantsala, P.Niemi, J.Metsa-Ketela, M.

(2014) Chem Biol 21: 1381-1391

  • DOI: https://doi.org/10.1016/j.chembiol.2014.07.017
  • Primary Citation of Related Structures:  
    4OSO, 4OSP

  • PubMed Abstract: 

    Angucyclines are tetracyclic polyketides produced by Streptomyces bacteria that exhibit notable biological activities. The great diversity of angucyclinones is generated in tailoring reactions, which modify the common benz[a]anthraquinone carbon skeleton. In particular, the opposite stereochemistry of landomycins and urdamycins/gaudimycins at C-6 is generated by the short-chain alcohol dehydrogenases/reductases LanV and UrdMred/CabV, respectively. Here we present crystal structures of LanV and UrdMred in complex with NADP(+) and the product analog rabelomycin, which enabled us to identify four regions associated with the functional differentiation. The structural analysis was confirmed in chimeragenesis experiments focusing on these regions adjacent to the active site cavity, which led to reversal of the activities of LanV and CabV. The results surprisingly indicated that the conformation of the substrate and the stereochemical outcome of 6-ketoreduction appear to be intimately linked.

  • Organizational Affiliation

    Department of Biochemistry, University of Turku, 20014 Turku, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
263Streptomyces fradiaeMutation(s): 0 
Gene Names: urdM
Find proteins for K0IB23 (Streptomyces fradiae)
Explore K0IB23 
Go to UniProtKB:  K0IB23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK0IB23
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
C21 H28 N7 O17 P3
Query on 2V4

Download Ideal Coordinates CCD File 
F [auth A]rabelomycin
C19 H14 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.44α = 90
b = 110.33β = 110.35
c = 78.07γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
EDNAdata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2014-12-03
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description