1JU2

Crystal structure of the hydroxynitrile lyase from almond


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

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: 803-815

  • DOI: https://doi.org/10.1016/s0969-2126(01)00639-6
  • Primary Citation of Related Structures:  
    1JU2

  • PubMed Abstract: 

    Cyanogenesis is a defense process of several thousand plant species. Hydroxynitrile lyase, a key enzyme of this process, cleaves a cyanohydrin into hydrocyanic acid and the corresponding aldehyde or ketone. The reverse reaction constitutes an important tool in biocatalysis. Different classes of hydroxynitrile lyases have convergently evolved from FAD-dependent oxidoreductases, alpha/beta hydrolases, and alcohol dehydrogenases. The FAD-dependent hydroxynitrile lyases (FAD-HNLs) carry a flavin cofactor whose redox properties appear to be unimportant for catalysis.


  • Organizational Affiliation

    Institut für Chemie, Karl-Franzens-Universität, Heinrichstrasse 28, Graz A-8010, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hydroxynitrile lyase
A, B
536Prunus dulcisMutation(s): 0 
EC: 4.1.2.10
UniProt
Find proteins for Q945K2 (Prunus dulcis)
Explore Q945K2 
Go to UniProtKB:  Q945K2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ945K2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
D, G
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83878UZ
GlyCosmos:  G83878UZ
GlyGen:  G83878UZ
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
E
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G16799JU
GlyCosmos:  G16799JU
GlyGen:  G16799JU
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
H
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G18638YB
GlyCosmos:  G18638YB
GlyGen:  G18638YB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.160 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.176α = 79.57
b = 67.494β = 77.78
c = 79.796γ = 67.19
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary