4OSP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1016/j.chembiol.2014.07.017
  • Primary Citation of Related Structures:  

  • 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 skel ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxygenase-reductase
A, B, C, D
263Streptomyces fradiaeMutation(s): 0 
Gene Names: urdM
Find proteins for K0IB23 (Streptomyces fradiae)
Go to UniProtKB:  K0IB23
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
2V4
Query on 2V4

Download SDF File 
Download CCD File 
A
rabelomycin
(3R)-3,6,8-trihydroxy-3-methyl-3,4-dihydrotetraphene-1,7,12(2H)-trione
C19 H14 O6
JJOLHRYZQSDLSA-LJQANCHMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.440α = 90.00
b = 110.330β = 110.35
c = 78.070γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction
EDNAdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Structure summary
  • Version 1.2: 2014-12-03
    Type: Database references
  • Version 1.3: 2017-10-11
    Type: Data collection