5EB5

The crystal structure of almond HNL, PaHNL5 V317A, in complex with benzyl alcohol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of almond hydroxynitrile lyase isoenzyme 5 provide a rationale for the lack of oxidoreductase activity in flavin dependent HNLs.

Pavkov-Keller, T.Bakhuis, J.Steinkellner, G.Jolink, F.Keijmel, E.Birner-Gruenberger, R.Gruber, K.

(2016) J.Biotechnol. 235: 24-31

  • DOI: 10.1016/j.jbiotec.2016.04.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hydroxynitrile lyases (HNLs) catalyze the asymmetric addition of HCN to aldehydes producing enantiomerically pure cyanohydrins. These enzymes can be heterologously expressed in large quantities making them interesting candidates for industrial applic ...

    Hydroxynitrile lyases (HNLs) catalyze the asymmetric addition of HCN to aldehydes producing enantiomerically pure cyanohydrins. These enzymes can be heterologously expressed in large quantities making them interesting candidates for industrial applications. The HNLs from Rosaceae evolved from flavin dependent dehydrogenase/oxidase structures. Here we report the high resolution X-ray structure of the highly glycosylated Prunus amygdalus HNL isoenzyme5 (PaHNL5 V317A) expressed in Aspergillus niger and its complex with benzyl alcohol. A comparison with the structure of isoenzyme PaHNL1 indicates a higher accessibility to the active site and a larger cavity for PaHNL5. Additionally, the PaHNL5 complex structure with benzyl alcohol was compared with the structurally related aryl-alcohol oxidase (AAO). Even though both enzymes contain an FAD-cofactor and histidine residues at crucial positions in the active site, PaHNL5 lacks the oxidoreductase activity. The structures indicate that in PaHNLs benzyl alcohol is bound too far away from the FAD cofactor in order to be oxidized.


    Organizational Affiliation

    ACIB GmbH, Petersgasse 14, 8010 Graz, Austria; Research Unit Functional Proteomics and Metabolic Pathways, Institute of Pathology, Medical University of Graz, Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.,ACIB GmbH, Petersgasse 14, 8010 Graz, Austria; Institute of Molecular Biosciences, University of Graz, Humboldtstra├če 50/3, 8010 Graz, Austria. Electronic address: karl.gruber@uni-graz.at.,ACIB GmbH, Petersgasse 14, 8010 Graz, Austria; Institute of Molecular Biosciences, University of Graz, Humboldtstra├če 50/3, 8010 Graz, Austria.,DSM, Alexander Flemingplaan 1, 2613 AX Delft, Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hnl isoenzyme 5
A, B
532Prunus dulcisMutation(s): 1 
Gene Names: MDL1
EC: 4.1.2.10
Find proteins for O24243 (Prunus dulcis)
Go to UniProtKB:  O24243
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
010
Query on 010

Download SDF File 
Download CCD File 
A, B
phenylmethanol
C7 H8 O
WVDDGKGOMKODPV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.364α = 90.00
b = 95.161β = 90.01
c = 92.190γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austria--

Revision History 

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2016-10-05
    Type: Database references