The crystal structure of angucycline C-6 ketoreductase LanV with bound NADP and 11-deoxy-6-oxylandomycinone

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structural and functional analysis of angucycline C-6 ketoreductase LanV involved in landomycin biosynthesis.

Paananen, P.Patrikainen, P.Kallio, P.Mantsala, P.Niemi, J.Niiranen, L.Metsa-Ketela, M.

(2013) Biochemistry 52: 5304-5314

  • DOI: https://doi.org/10.1021/bi400712q
  • Primary Citation of Related Structures:  
    4KWH, 4KWI

  • PubMed Abstract: 

    Angucyclines are biologically active natural products constructed around a common benz[a]anthraquinone carbon frame. One key branching point in the biosynthesis of angucyclines is the ketoreduction at C-6, which results in the opposite stereochemistry of landomycins and urdamycins/gaudimycins. Here we present the 1.65 Å resolution crystal structure of LanV from Streptomyces cyanogenus S136 that is responsible for the 6R stereochemistry of landomycins. The enzyme displays the common architectural fold of short-chain alcohol dehydrogenases/reductases and contains bound nicotinamide adenine dinucleotide phosphate. Determination of the structure of LanV in complex with 11-deoxylandomycinone at 2.0 Å resolution indicated that substrate binding does not induce large conformational changes and that substrate recognition occurs mainly through hydrophobic interactions. Analysis of the electron density map of the ternary complex revealed that the catalytic reaction had most likely proceeded backward in the crystal, because the data could be best fit with a compound harboring a carbonyl group at C-6. A coordinated water molecule was atypically identified between the ligand and the conserved Tyr160 residue, which was confirmed to be critical for the catalytic activity by site-directed mutagenesis. A catalytic triad of Ser147, Tyr160, and Lys164 could be recognized on the basis of the crystal structure, and stereoselective labeling studies demonstrated that the transfer of hydride from reduced nicotinamide adenine dinucleotide phosphate to the substrate occurs from the 4-pro-S side of the cosubstrate. Importantly, Ser192 was identified as being involved in controlling the stereochemistry of the reaction, as assays with single mutant Ser192Ile led to accumulation of gaudimycin C with 6S stereochemistry as a minor product.

  • Organizational Affiliation

    Department of Biochemistry and Food Chemistry, University of Turku , FIN-20014 Turku, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reductase homolog
A, B
263Streptomyces cyanogenusMutation(s): 0 
Gene Names: lanV
Find proteins for Q9ZGC1 (Streptomyces cyanogenus)
Explore Q9ZGC1 
Go to UniProtKB:  Q9ZGC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZGC1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.61α = 90
b = 92.61β = 90
c = 106.33γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MxCuBEdata collection
EDNAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description