4OSP | pdb_00004osp

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 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.chembiol.2014.07.017
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 112.4 kDa 
  • Atom Count: 7,680 
  • Modeled Residue Count: 1,002 
  • Deposited Residue Count: 1,052 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygenase-reductase
A, B, C, D
263Streptomyces fradiaeMutation(s): 0 
Gene Names: urdM
UniProt
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP



Download:Ideal Coordinates CCD File
E [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
2V4

Query on 2V4



Download:Ideal Coordinates CCD File
F [auth A]rabelomycin
C19 H14 O6
JJOLHRYZQSDLSA-LJQANCHMSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
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
MOLREPphasing
REFMACrefinement
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