7YAS

HYDROXYNITRILE LYASE, LOW TEMPERATURE NATIVE STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis.

Zuegg, J.Gruber, K.Gugganig, M.Wagner, U.G.Kratky, C.

(1999) Protein Sci 8: 1990-2000

  • DOI: 10.1110/ps.8.10.1990
  • Primary Citation of Related Structures:  
    2YAS, 3YAS, 4YAS, 5YAS, 6YAS, 7YAS

  • PubMed 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 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.


    Related Citations: 
    • Hydroxynitrile Lyase from Hevea brasiliensis: Molecular Characterization and Mechanism of Enzyme Catalysis
      Hasslacher, M., Kratky, C., Griengl, H., Schwab, H., Kohlwein, S.D.
      (1997) Proteins 27: 438
    • Mechanism of Cyanogenesis: The Crystal Structure of Hydroxynitrile Lyase from Hevea brasiliensis
      Wagner, U.G., Hasslacher, M., Griengl, H., Schwab, H., Kratky, C.
      (1996) Structure 4: 811
    • Crystallization and preliminary X-ray diffraction studies of a hydroxynitrile lyase from Hevea brasiliensis.
      Wagner, U.G., Schall, M., Hasslacher, M., Hayn, M., Griengl, H., Schwab, H., Kratky, C.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 591
    • Molecular Cloning of the Full-Length Cdna of (S)-Hydroxynitrile Lyase from Hevea brasiliensis. Functional Expression in Escherichia coli and Saccharomyces cerevisiae and Identification of an Active Site Residue
      Hasslacher, M., Schall, M., Hayn, M., Griengl, H., Kohlwein, S.D., Schwab, H.
      (1996) J Biol Chem 271: 5884

    Organizational Affiliation

    Abteilung für Strukturbiologie, Institut für Physikalische Chemie, Karl-Franzens Universität Graz, Austria.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HYDROXYNITRILE LYASE)A257Hevea brasiliensisMutation(s): 0 
Gene Names: HNL
EC: 4.1.2.39 (PDB Primary Data), 4.1.2.47 (UniProt)
UniProt
Find proteins for P52704 (Hevea brasiliensis)
Explore P52704 
Go to UniProtKB:  P52704
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52704
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.529α = 90
b = 106.434β = 90
c = 128.381γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references