Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 139.40 kDa 
• Atom Count: 8768 
• Residue Count: 1248 
• Unique protein chains: 1

4BIF

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

• DOI: 10.2210/pdb4BIF/pdb

• Classification: LYASE
• Organism(s): Granulicella tundricola MP5ACTX9
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-10 Released: 2013-09-11 
• Deposition Author(s): Hajnal, I., Lyskowski, A., Hanefeld, U., Gruber, K., Schwab, H., Steiner, K.

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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 

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

• PubMed: 23981508 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN	A, B, C, D, E, F, G, H	156	Granulicella tundricola MP5ACTX9	Mutation(s): 0  Gene Names: AciX9_0562
Find proteins for E8WYN5 (Granulicella tundricola (strain ATCC BAA-1859 / DSM 23138 / MP5ACTX9)) Explore E8WYN5  Go to UniProtKB:  E8WYN5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	A, B, C, D, E, F, G, H	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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 = 126.31	α = 90
b = 254.78	β = 90
c = 82.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
xia2	data reduction
XSCALE	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-10 
• Released Date: 2013-09-11 
Deposition Author(s): Hajnal, I., Lyskowski, A., Hanefeld, U., Gruber, K., Schwab, H., Steiner, K.

Revision History 

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