PDBsum entry 1ju2

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Lyase PDB id
Protein chains
521 a.a. *
NAG ×2
FAD ×2
IPA ×2
Waters ×1516
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of the hydroxynitrile lyase from almond
Structure: Hydroxynitrile lyase. Chain: a, b. Ec:
Source: Prunus dulcis. Almond. Organism_taxid: 3755
1.47Å     R-factor:   0.160     R-free:   0.186
Authors: I.Dreveny,K.Gruber,A.Glieder,A.Thompson,C.Kratky
Key ref:
I.Dreveny et al. (2001). The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase. Structure, 9, 803-815. PubMed id: 11566130 DOI: 10.1016/S0969-2126(01)00639-6
23-Aug-01     Release date:   04-Sep-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q945K2  (Q945K2_PRUDU) -  (R)-mandelonitrile lyase 2
563 a.a.
521 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - (R)-mandelonitrile lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (R)-mandelonitrile = cyanide + benzaldehyde
= cyanide
+ benzaldehyde
      Cofactor: Flavoprotein
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     lyase activity     4 terms  


    Added reference    
DOI no: 10.1016/S0969-2126(01)00639-6 Structure 9:803-815 (2001)
PubMed id: 11566130  
The hydroxynitrile lyase from almond: a lyase that looks like an oxidoreductase.
I.Dreveny, K.Gruber, A.Glieder, A.Thompson, C.Kratky.
BACKGROUND: 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. RESULTS: We have determined the crystal structure of a 61 kDa hydroxynitrile lyase isoenzyme from Prunus amygdalus (PaHNL1) to 1.5 A resolution. Clear electron density originating from four glycosylation sites could be observed. As concerns the overall protein fold including the FAD cofactor, PaHNL1 belongs to the family of GMC oxidoreductases. The active site for the HNL reaction is probably at a very similar position as the active sites in homologous oxidases. CONCLUSIONS: There is strong evidence from the structure and the reaction product that FAD-dependent hydroxynitrile lyases have evolved from an aryl alcohol oxidizing precursor. Since key residues implicated in oxidoreductase activity are also present in PaHNL1, it is not obvious why this enzyme shows no oxidase activity. Similarly, features proposed to be relevant for hydroxy-nitrile lyase activity in other hydroxynitrile lyases, i.e., a general base and a positive charge to stabilize the cyanide, are not obviously present in the putative active site of PaHNL1. Therefore, the reason for its HNL activity is far from being well understood at this point.
  Selected figure(s)  
Figure 1.
Figure 1. The Biological Role of Hydroxynitrile Lyases in Plant Cyanogenesis

  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 803-815) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21307605 Y.Fukuta, S.Nanda, Y.Kato, H.Yurimoto, Y.Sakai, H.Komeda, and Y.Asano (2011).
Characterization of a new (R)-hydroxynitrile lyase from the Japanese apricot Prunus mume and cDNA cloning and secretory expression of one of the isozymes in Pichia pastoris.
  Biosci Biotechnol Biochem, 75, 214-220.  
20467737 D.Ribitsch, S.Winkler, K.Gruber, W.Karl, E.Wehrschütz-Sigl, I.Eiteljörg, P.Schratl, P.Remler, R.Stehr, C.Bessler, N.Mussmann, K.Sauter, K.H.Maurer, and H.Schwab (2010).
Engineering of choline oxidase from Arthrobacter nicotianae for potential use as biological bleach in detergents.
  Appl Microbiol Biotechnol, 87, 1743-1752.  
19256550 I.Dreveny, A.S.Andryushkova, A.Glieder, K.Gruber, and C.Kratky (2009).
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.
  Biochemistry, 48, 3370-3377.
PDB codes: 3gdn 3gdp
19716614 J.N.Andexer, J.V.Langermann, U.Kragl, and M.Pohl (2009).
How to overcome limitations in biotechnological processes - examples from hydroxynitrile lyase applications.
  Trends Biotechnol, 27, 599-607.  
19574295 L.A.Kelley, P.J.Shrimpton, S.H.Muggleton, and M.J.Sternberg (2009).
Discovering rules for protein-ligand specificity using support vector inductive logic programming.
  Protein Eng Des Sel, 22, 561-567.  
19574215 P.Ferreira, A.Hernandez-Ortega, B.Herguedas, A.T.Martínez, and M.Medina (2009).
Aryl-alcohol oxidase involved in lignin degradation: a mechanistic study based on steady and pre-steady state kinetics and primary and solvent isotope effects with two alcohol substrates.
  J Biol Chem, 284, 24840-24847.  
18482980 C.Michalski, H.Mohagheghi, M.Nimtz, J.Pasteels, and D.Ober (2008).
Salicyl alcohol oxidase of the chemical defense secretion of two chrysomelid leaf beetles. Molecular and functional characterization of two new members of the glucose-methanol-choline oxidoreductase gene family.
  J Biol Chem, 283, 19219-19228.  
18540101 T.Ueatrongchit, A.Kayo, H.Komeda, Y.Asano, and A.H-Kittikun (2008).
Purification and characterization of a novel (R)-hydroxynitrile lyase from Eriobotrya japonica (Loquat).
  Biosci Biotechnol Biochem, 72, 1513-1522.  
18058961 Z.Liu, B.Pscheidt, M.Avi, R.Gaisberger, F.S.Hartner, C.Schuster, W.Skranc, K.Gruber, and A.Glieder (2008).
Laboratory evolved biocatalysts for stereoselective syntheses of substituted benzaldehyde cyanohydrins.
  Chembiochem, 9, 58-61.  
17498303 K.Iida, D.L.Cox-Foster, X.Yang, W.Y.Ko, and D.R.Cavener (2007).
Expansion and evolution of insect GMC oxidoreductases.
  BMC Evol Biol, 7, 75.  
17607575 T.Purkarthofer, W.Skranc, C.Schuster, and H.Griengl (2007).
Potential and capabilities of hydroxynitrile lyases as biocatalysts in the chemical industry.
  Appl Microbiol Biotechnol, 76, 309-320.  
16999821 P.Ferreira, F.J.Ruiz-Dueñas, M.J.Martínez, W.J.van Berkel, and A.T.Martínez (2006).
Site-directed mutagenesis of selected residues at the active site of aryl-alcohol oxidase, an H2O2-producing ligninolytic enzyme.
  FEBS J, 273, 4878-4888.  
16404574 S.Kurdyukov, A.Faust, S.Trenkamp, S.Bär, R.Franke, N.Efremova, K.Tietjen, L.Schreiber, H.Saedler, and A.Yephremov (2006).
Genetic and biochemical evidence for involvement of HOTHEAD in the biosynthesis of long-chain alpha-,omega-dicarboxylic fatty acids and formation of extracellular matrix.
  Planta, 224, 315-329.  
15999392 R.Weis, R.Gaisberger, W.Skranc, K.Gruber, and A.Glieder (2005).
Carving the active site of almond R-HNL for increased enantioselectivity.
  Angew Chem Int Ed Engl, 44, 4700-4704.  
14557277 S.S.Pang, R.G.Duggleby, R.L.Schowen, and L.W.Guddat (2004).
The crystal structures of Klebsiella pneumoniae acetolactate synthase with enzyme-bound cofactor and with an unusual intermediate.
  J Biol Chem, 279, 2242-2253.
PDB codes: 1n0h 1ozf 1ozg 1ozh
12899689 H.Riveros-Rosas, A.Julián-Sánchez, R.Villalobos-Molina, J.P.Pardo, and E.Piña (2003).
Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily.
  Eur J Biochem, 270, 3309-3334.  
12904212 K.A.Krolikowski, J.L.Victor, T.N.Wagler, S.J.Lolle, and R.E.Pruitt (2003).
Isolation and characterization of the Arabidopsis organ fusion gene HOTHEAD.
  Plant J, 35, 501-511.  
11790839 I.Dreveny, C.Kratky, and K.Gruber (2002).
The active site of hydroxynitrile lyase from Prunus amygdalus: modeling studies provide new insights into the mechanism of cyanogenesis.
  Protein Sci, 11, 292-300.  
11992525 L.G.Cascão Pereira, A.Hickel, C.J.Radke, and H.W.Blanch (2002).
A kinetic model for enzyme interfacial activity and stability: pa-hydroxynitrile lyase at the diisopropyl ether/water interface.
  Biotechnol Bioeng, 78, 595-605.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.