Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 97.86 kDa 
• Atom Count: 7159 
• Modelled Residue Count: 866 
• Deposited Residue Count: 908 
• Unique protein chains: 1

4AO9

Biochemical properties and crystal structure of a novel beta- phenylalanine aminotransferase from Variovorax paradoxus

• PDB DOI: 10.2210/pdb4AO9/pdb

• Classification: TRANSFERASE
• Organism(s): Variovorax paradoxus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-25 Released: 2012-10-24 
• Deposition Author(s): Crismaru, C.G., Wybenga, G.G., Szymanski, W., Wijma, H.J., Wu, B., deWildeman, S., Poelarends, G.J., Dijkstra, B.W., Janssen, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.182 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

Biochemical Properties and Crystal Structure of a Novel Beta-Phenylalanine Aminotransferase from Variovorax Paradoxus

Crismaru, C.G., Wybenga, G.G., Szymanski, W., Wijma, H.J., Wu, B., Dewildeman, S., Poelarends, G.J., Dijkstra, B.W., Janssen, D.B.

(2013) Appl Environ Microbiol 79: 185

• PubMed: 23087034 
• DOI: 10.1128/AEM.02525-12
• Primary Citation of Related Structures:  
  4AO9, 4AOA


• PubMed Abstract: 
  

By selective enrichment, we isolated a bacterium that can use β-phenylalanine as a sole nitrogen source. It was identified by 16S rRNA gene sequencing as a strain of Variovorax paradoxus. Enzyme assays revealed an aminotransferase activity. Partial genome sequencing and screening of a cosmid DNA library resulted in the identification of a 1,302-bp aminotransferase gene, which encodes a 46,416-Da protein. The gene was cloned and overexpressed in Escherichia coli. The recombinant enzyme was purified and showed a specific activity of 17.5 U mg(-1) for (S)-β-phenylalanine at 30°C and 33 U mg(-1) at the optimum temperature of 55°C. The β-specific aminotransferase exhibits a broad substrate range, accepting ortho-, meta-, and para-substituted β-phenylalanine derivatives as amino donors and 2-oxoglutarate and pyruvate as amino acceptors. The enzyme is highly enantioselective toward (S)-β-phenylalanine (enantioselectivity [E], >100) and derivatives thereof with different substituents on the phenyl ring, allowing the kinetic resolution of various racemic β-amino acids to yield (R)-β-amino acids with >95% enantiomeric excess (ee). The crystal structures of the holoenzyme and of the enzyme in complex with the inhibitor 2-aminooxyacetate revealed structural similarity to the β-phenylalanine aminotransferase from Mesorhizobium sp. strain LUK. The crystal structure was used to rationalize the stereo- and regioselectivity of V. paradoxus aminotransferase and to define a sequence motif with which new aromatic β-amino acid-converting aminotransferases may be identified.

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Organizational Affiliation: 

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-PHENYLALANINE AMINOTRANSFERASE	A, B	454	Variovorax paradoxus	Mutation(s): 0  EC: 2.6.1
UniProt
Find proteins for H8WR05 (Variovorax paradoxus) Explore H8WR05  Go to UniProtKB:  H8WR05

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.182 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.74	α = 90
b = 100.11	β = 90
c = 104.799	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-25 
• Released Date: 2012-10-24 
Deposition Author(s): Crismaru, C.G., Wybenga, G.G., Szymanski, W., Wijma, H.J., Wu, B., deWildeman, S., Poelarends, G.J., Dijkstra, B.W., Janssen, D.B.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2012-11-07
  Changes: Database references
• Version 1.2: 2012-11-14
  Changes: Other
• Version 1.3: 2013-01-16
  Changes: Database references