4BIF

Biochemical and structural characterisation of a novel manganese- dependent hydroxynitrile lyase from bacteria


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biochemical and Structural Characterisation of a Novel Bacterial Manganese-Dependent Hydroxynitrile Lyase.

Hajnal, I.Lyskowski, A.Hanefeld, U.Gruber, K.Schwab, H.Steiner, K.

(2013) FEBS J. 280: 5815

  • DOI: 10.1111/febs.12501

  • PubMed Abstract: 
  • Hydroxynitrile lyases (HNLs), which catalyse the decomposition of cyanohydrins, are found mainly in plants. In vitro, they are able to catalyse the synthesis of enantiopure cyanohydrins, which are versatile building blocks in the chemical industry. R ...

    Hydroxynitrile lyases (HNLs), which catalyse the decomposition of cyanohydrins, are found mainly in plants. In vitro, they are able to catalyse the synthesis of enantiopure cyanohydrins, which are versatile building blocks in the chemical industry. Recently, HNLs have also been discovered in bacteria. Here, we report on the detailed biochemical and structural characterization of a hydroxynitrile lyase from Granulicella tundricola (GtHNL), which was successfully heterologously expressed in Escherichia coli. The crystal structure was solved at a crystallographic resolution of 2.5 Å and exhibits a cupin fold. As GtHNL does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs, cupins represent a new class of HNLs. GtHNL is metal-dependent, as confirmed by inductively coupled plasma/optical emission spectroscopy, and in the crystal structure, manganese is bound to three histidine and one glutamine residue. GtHNL displayed a specific activity of 1.74 U·mg(-1) at pH 6 with (R)-mandelonitrile, and synthesized (R)-mandelonitrile with 90% enantiomeric excess at 80% conversion using 0.5 m benzaldehyde in a biphasic reaction system with methyl tertiary butyl ether.


    Related Citations: 
    • Crystallization of a Novel Metal-Containing Cupin from Acidobacterium Sp. And Preliminary Diffraction Data Analysis.
      Lyskowski, A.,Steiner, K.,Hajnal, I.,Steinkellner, G.,Schwab, H.,Gruber, K.
      (2012) Acta Crystallogr.,Sect.F 68: 451


    Organizational Affiliation

    Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria; Gebouw voor Scheikunde, Technische Universiteit Delft, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN
A, B, C, D, E, F, G, H
156Granulicella tundricola (strain ATCC BAA-1859 / DSM 23138 / MP5ACTX9)Mutation(s): 0 
Find proteins for E8WYN5 (Granulicella tundricola (strain ATCC BAA-1859 / DSM 23138 / MP5ACTX9))
Go to UniProtKB:  E8WYN5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 126.310α = 90.00
b = 254.780β = 90.00
c = 82.470γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
xia2data reduction
BALBESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references