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PDBsum entry 5yas
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Lyase PDB id
5yas

 

 

 

 

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Contents
Protein chain
256 a.a. *
Ligands
SO4 ×4
FAC
Waters ×342
* Residue conservation analysis
PDB id:
5yas
Name: Lyase
Title: Hydroxynitrile lyase complexed with hexafluoroacetone
Structure: Protein (hydroxynitrile lyase). Chain: a. Synonym: oxynitrilase. Engineered: yes
Source: Hevea brasiliensis. Organism_taxid: 3981. Organ: leaf. Gene: hnl. Expressed in: pichia pastoris. Expression_system_taxid: 4922.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.187     R-free:   0.241
Authors: J.Zuegg,U.G.Wagner,M.Gugganig,C.Kratky
Key ref:
J.Zuegg et al. (1999). Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis. Protein Sci, 8, 1990-2000. PubMed id: 10548044 DOI: 10.1110/ps.8.10.1990
Date:
15-Mar-99     Release date:   13-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P52704  (HNL_HEVBR) -  (S)-hydroxynitrile lyase from Hevea brasiliensis
Seq:
Struc: 		257 a.a.
256 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.2.47  - (S)-hydroxynitrile lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. a monosubstituted aliphatic (S)-hydroxynitrile = an aldehyde + hydrogen cyanide
2. a disubstituted aliphatic (S)-hydroxynitrile = a ketone + hydrogen cyanide
3. an aromatic (S)-hydroxynitrile = an aromatic aldehyde + hydrogen cyanide
monosubstituted aliphatic (S)-hydroxynitrile
 = aldehyde
 + hydrogen cyanide
disubstituted aliphatic (S)-hydroxynitrile
 = ketone
 + hydrogen cyanide
aromatic (S)-hydroxynitrile
 = aromatic aldehyde
 + hydrogen cyanide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1110/ps.8.10.1990 Protein Sci 8:1990-2000 (1999)
PubMed id: 10548044  
 
 
Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis.
J.Zuegg, K.Gruber, M.Gugganig, U.G.Wagner, C.Kratky.
 
  ABSTRACT  
 
The 3D structures of complexes between the hydroxynitrile lyase from Hevea brasiliensis (Hb-HNL) and several substrate and/or inhibitor molecules, including trichloracetaldehyde, hexafluoracetone, acetone, and rhodanide, were determined by X-ray crystallography. The complex with trichloracetaldehyde showed a covalent linkage between the protein and the inhibitor, which had apparently resulted from nucleophilic attack of the catalytic Ser80-Ogamma. All other complexes showed the substrate or inhibitor molecule merely hydrogen bonded to the protein. In addition, the native crystal structure of Hb-HNL was redetermined at cryo-temperature and at room temperature, eliminating previous uncertainties concerning residual electron density within the active site, and leading to the observation of two conserved water molecules. One of them was found to be conserved in all complex structures and appears to have mainly structural significance. The other water molecule is conserved in all structures except for the complex with rhodanide; it is hydrogen bonded to the imidazole of the catalytic His235 and appears to affect the Hb-HNL catalyzed reaction. The observed 3D structural data suggest implications for the enzyme mechanism. It appears that the enzyme-catalyzed cyanohydrin formation is unlikely to proceed via a hemiacetal or hemiketal intermediate covalently attached to the enzyme, despite the observation of such an intermediate for the complex with trichloracetaldehyde. Instead, the data are consistent with a mechanism where the incoming substrate is activated by hydrogen bonding with its carbonyl oxygen to the Ser80 and Thr11 hydroxy groups. A hydrogen cyanide molecule subsequently replaces a water molecule and is deprotonated presumably by the His235 base. Deprotonation is facilitated by the proximity of the positive charge of the Lys236 side chain.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. Residual density within the active site of Hb--HNL for the ~A! F6-acetone, ~B! rhodanide, and ~C! acetone soaks. See caption to Figure 3 for details.
 
  The above figure is reprinted by permission from the Protein Society: Protein Sci (1999, 8, 1990-2000) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
18498103 D.C.Bas, D.M.Rogers, and J.H.Jensen (2008).
Very fast prediction and rationalization of pKa values for protein-ligand complexes.
  Proteins, 73, 765-783.  
19006143 M.Avi, R.M.Wiedner, H.Griengl, and H.Schwab (2008).
Improvement of a stereoselective biocatalytic synthesis by substrate and enzyme engineering: 2-hydroxy-(4'-oxocyclohexyl)acetonitrile as the model.
  Chemistry, 14, 11415-11422.  
18449577 Q.Luo, W.W.Han, Y.H.Zhou, Y.Yao, and Z.S.Li (2008).
The 3D structure of the defense-related rice protein Pir7b predicted by homology modeling and ligand binding studies.
  J Mol Model, 14, 559-569.  
17252134 J.J.Li, and T.D.Bugg (2007).
Investigation of a general base mechanism for ester hydrolysis in C-C hydrolase enzymes of the alpha/beta-hydrolase superfamily: a novel mechanism for the serine catalytic triad.
  Org Biomol Chem, 5, 507-513.  
17075950 B.D.Charette, R.G.Macdonald, S.Wetzel, D.B.Berkowitz, and H.Waldmann (2006).
Protein structure similarity clustering: dynamic treatment of PDB structures facilitates clustering.
  Angew Chem Int Ed Engl, 45, 7766-7770.  
16634109 T.Purkarthofer, K.Gruber, M.Gruber-Khadjawi, K.Waich, W.Skranc, D.Mink, and H.Griengl (2006).
A biocatalytic Henry reaction--the hydroxynitrile lyase from Hevea brasiliensis also catalyzes nitroaldol reactions.
  Angew Chem Int Ed Engl, 45, 3454-3456.  
15309340 R.Xu, M.H.Zong, Y.Y.Liu, J.He, Y.Y.Zhang, and W.Y.Lou (2004).
Enzymatic enantioselective transcyanation of silicon-containing aliphatic ketone with (S)-hydroxynitrile lyase from Manihot esculenta.
  Appl Microbiol Biotechnol, 66, 27-33.  
12616635 H.Bühler, F.Effenberger, S.Förster, J.Roos, and H.Wajant (2003).
Substrate specificity of mutants of the hydroxynitrile lyase from Manihot esculenta.
  Chembiochem, 4, 211-216.  
11173464 H.Lauble, S.Förster, B.Miehlich, H.Wajant, and F.Effenberger (2001).
Structure of hydroxynitrile lyase from Manihot esculenta in complex with substrates acetone and chloroacetone: implications for the mechanism of cyanogenesis.
  Acta Crystallogr D Biol Crystallogr, 57, 194-200.
PDB codes: 1dwo 1dwp 1dwq
10679367 D.V.Johnson, A.A.Zabelinskaja-Mackova, and H.Griengl (2000).
Oxynitrilases for asymmetric C-C bond formation.
  Curr Opin Chem Biol, 4, 103-109.  
11102786 F.Effenberger, S.Förster, and H.Wajant (2000).
Hydroxynitrile lyases in stereoselective catalysis.
  Curr Opin Biotechnol, 11, 532-539.  
10802560 H.Griengl, H.Schwab, and M.Fechter (2000).
The synthesis of chiral cyanohydrins by oxynitrilases.
  Trends Biotechnol, 18, 252-256.  
10679382 R.J.Kazlauskas (2000).
Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities.
  Curr Opin Chem Biol, 4, 81-88.  
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.

 

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