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 
  • R-Value Observed: 0.177 

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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
  • Primary Citation of Related Structures:  
    4BIF

  • 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. Recently, HNLs have also been discovered in bacteria ...

    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 Struct Biol Cryst Commun 68: 451
    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
156Granulicella tundricola MP5ACTX9Mutation(s): 0 
Gene Names: AciX9_0562
UniProt
Find proteins for E8WYN5 (Granulicella tundricola (strain ATCC BAA-1859 / DSM 23138 / MP5ACTX9))
Explore E8WYN5 
Go to UniProtKB:  E8WYN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE8WYN5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.31α = 90
b = 254.78β = 90
c = 82.47γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
xia2data reduction
XSCALEdata scaling
BALBESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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