3GDN

Almond hydroxynitrile lyase in complex with benzaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substrate binding in the FAD-dependent hydroxynitrile lyase from almond provides insight into the mechanism of cyanohydrin formation and explains the absence of dehydrogenation activity.

Dreveny, I.Andryushkova, A.S.Glieder, A.Gruber, K.Kratky, C.

(2009) Biochemistry 48: 3370-3377

  • DOI: 10.1021/bi802162s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In a large number of plant species hydroxynitrile lyases catalyze the decomposition of cyanohydrins in order to generate hydrogen cyanide upon tissue damage. Hydrogen cyanide serves as a deterrent against herbivores and fungi. In vitro hydroxynitrile ...

    In a large number of plant species hydroxynitrile lyases catalyze the decomposition of cyanohydrins in order to generate hydrogen cyanide upon tissue damage. Hydrogen cyanide serves as a deterrent against herbivores and fungi. In vitro hydroxynitrile lyases are proficient biocatalysts for the stereospecific synthesis of cyanohydrins. Curiously, hydroxynitrile lyases from different species are completely unrelated in structure and substrate specificity despite catalyzing the same reaction. The hydroxynitrile lyase from almond shows close resemblance to flavoproteins of the glucose-methanol-choline oxidoreductase family. We report here 3D structural data of this lyase with the reaction product benzaldehyde bound within the active site, which allow unambiguous assignment of the location of substrate binding. Based on the binding geometry, a reaction mechanism is proposed that involves one of the two conserved active site histidine residues acting as a general base abstracting the proton from the cyanohydrin hydroxyl group. Site-directed mutagenesis shows that both active site histidines are required for the reaction to occur. There is no evidence that the flavin cofactor directly participates in the reaction. Comparison with other hydroxynitrile lyases reveals a large diversity of active site architectures, which, however, share the common features of a general active site base and a nearby patch with positive electrostatic potential. On the basis of the difference in substrate binding geometry between the FAD-dependent HNL from almond and the related oxidases, we can rationalize why the HNL does not act as an oxidase.


    Related Citations: 
    • The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase.
      Dreveny, I.,Gruber, K.,Glieder, A.,Thompson, A.,Kratky, C.
      (2001) Structure 9: 803


    Organizational Affiliation

    Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Humboldtstrasse 50/III, A-8010 Graz, Austria. ingrid.dreveny@nottingham.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
R-oxynitrile lyase isoenzyme 1
A, B
521Prunus dulcisMutation(s): 0 
Gene Names: MDL2 (HNL1)
EC: 4.1.2.10
Find proteins for Q945K2 (Prunus dulcis)
Go to UniProtKB:  Q945K2
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MXN
Query on MXN

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Download CCD File 
A, B
(2R)-hydroxy(phenyl)ethanenitrile
(R)-mandelonitrile
C8 H7 N O
NNICRUQPODTGRU-QMMMGPOBSA-N
 Ligand Interaction
HBX
Query on HBX

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A, B
benzaldehyde
C7 H6 O
HUMNYLRZRPPJDN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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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: 1.67 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.980α = 90.00
b = 93.790β = 106.47
c = 86.900γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345dtbdata collection
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance