1DWO

Crystal Structure of Hydroxynitrile Lyase from Manihot esculenta in Complex with Substrates Acetone and Chloroacetone:Implications for the Mechanism of Cyanogenesis

• PDB DOI: https://doi.org/10.2210/pdb1DWO/pdb

• Classification: HYDROXYNITRILE LYASE
• Organism(s): Manihot esculenta
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-12-10 Released: 2000-12-07 
• Deposition Author(s): Lauble, H., Forster, S., Miehlich, B., Wajant, H., Effenberger, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

Structure of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Substrates Acetone and Chloroacetone: Implications for the Mechanism of Cyanogenesis

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

(2001) Acta Crystallogr D Biol Crystallogr 57: 194

• PubMed: 11173464 
• DOI: https://doi.org/10.1107/s0907444900015766
• Primary Citation of Related Structures:  
  1DWO, 1DWP, 1DWQ


• PubMed Abstract: 
  

  The crystal structures of hydroxynitrile lyase from Manihot esculenta (MeHNL) complexed with the native substrate acetone and substrate analogue chloroacetone have been determined and refined at 2.2 A resolution. The substrates are positioned in the active site by hydrogen-bond interactions of the carbonyl O atom with Thr11 OG, Ser80 OG and, to a lesser extent, Cys81 SG. These studies support a mechanism for cyanogenesis as well as for the stereospecific MeHNL-catalyzed formation of (S)-cyanohydrins, which closely resembles the base-catalyzed chemical reaction of HCN with carbonyl compounds.

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Organizational Affiliation: 

Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, D-70569 Stuttgart, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 59.73 kDa 
• Atom Count: 4,453 
• Modelled Residue Count: 520 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYNITRILE LYASE	A, B	262	Manihot esculenta	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACN	C [auth A]	ACETONE C3 H6 O CSCPPACGZOOCGX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.5	α = 90
b = 105.5	β = 90
c = 188.5	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-07 
Deposition Author(s): Lauble, H., Forster, S., Miehlich, B., Wajant, H., Effenberger, F.

Revision History  

• Version 1.0: 2000-12-07
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references