4KWH

The crystal structure of angucycline C-6 ketoreductase LanV with bound NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/bi400712q
  • Primary Citation of Related Structures:  

  • 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 stereochemistr ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reductase homolog
A, B
263Streptomyces cyanogenusMutation(s): 0 
Gene Names: lanV
Find proteins for Q9ZGC1 (Streptomyces cyanogenus)
Go to UniProtKB:  Q9ZGC1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

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

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.147 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.500α = 90.00
b = 92.500β = 90.00
c = 106.300γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
BALBESphasing
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references
  • Version 1.2: 2014-11-12
    Type: Structure summary