1E8D

MECHANISTIC ASPECTS OF CYANOGENESIS FROM ACTIVE SITE MUTANT SER80ALA OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN COMPLEX WITH ACETONE CYANOHYDRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanistic Aspects of Cyanogenesis from Active-Site Mutant Ser80Ala of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Acetone Cyanohydrin.

Lauble, H.Miehlich, B.Forster, S.Wajant, H.Effenberger, F.

(2001) Protein Sci 10: 1015

  • DOI: 10.1110/ps.01301
  • Primary Citation of Related Structures:  
    1E89, 1E8D

  • PubMed Abstract: 
  • The structure and function of hydroxynitrile lyase from Manihot esculenta (MeHNL) have been analyzed by X-ray crystallography and site-directed mutagenesis. The crystal structure of the MeHNL-S80A mutant enzyme has been refined to an R-factor of 18.0% against diffraction data to 2 ...

    The structure and function of hydroxynitrile lyase from Manihot esculenta (MeHNL) have been analyzed by X-ray crystallography and site-directed mutagenesis. The crystal structure of the MeHNL-S80A mutant enzyme has been refined to an R-factor of 18.0% against diffraction data to 2.1-A resolution. The three-dimensional structure of the MeHNL-S80A-acetone cyanohydrin complex was determined at 2.2-A resolution and refined to an R-factor of 18.7%. Thr11 and Cys81 involved in substrate binding have been substituted by Ala in site-directed mutagenesis. The kinetic measurements of these mutant enzymes are presented. Combined with structural data, the results support a mechanism for cyanogenesis in which His236 as a general base abstracts a proton from Ser80, thereby allowing proton transfer from the hydroxyl group of acetone cyanohydrin to Ser80. The His236 imidazolium cation then facilitates the leaving of the nitrile group by proton donating.


    Related Citations: 
    • Structure of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Substrates Acetone and Chloroacetone: Implications for the Mechanism of Cyanogenesis
      Lauble, H., Foerster, S., Miehlich, B., Wajant, H., Effenberger, F.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 194

    Organizational Affiliation

    Institut für Organische Chemie der Universität Stuttgart, D-70569 Stuttgart, Germany. PeterLauble@t-online.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROXYNITRILE LYASEA, B262Manihot esculentaMutation(s): 1 
Gene Names: HNL
EC: 4.2.1.37 (PDB Primary Data), 4.1.2.47 (UniProt)
UniProt
Find proteins for P52705 (Manihot esculenta)
Explore P52705 
Go to UniProtKB:  P52705
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNH
Query on CNH

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth B]2-HYDROXY-2-METHYLPROPANENITRILE
C4 H7 N O
MWFMGBPGAXYFAR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.9α = 90
b = 105.9β = 90
c = 187.8γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-17
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection