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: 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hydroxynitrile lyaseA, B536Prunus dulcisMutation(s): 0 
Gene Names: MDL2, HNL1
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseD, G 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G83878UZ
GlyCosmos:  G83878UZ
GlyGen:  G83878UZ
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseE 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G16799JU
GlyCosmos:  G16799JU
GlyGen:  G16799JU
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseH 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G18638YB
GlyCosmos:  G18638YB
GlyGen:  G18638YB
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
J [auth A],
M [auth B]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
IPA
Query on IPA
Download Ideal Coordinates CCD File 
K [auth A],
N [auth B]		ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N		 Ligand Interaction
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

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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