4AO4

Structural Determinants of the beta-Selectivity of a Bacterial Aminotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural determinants of the beta-selectivity of a bacterial aminotransferase.

Wybenga, G.G.Crismaru, C.G.Janssen, D.B.Dijkstra, B.W.

(2012) J. Biol. Chem. 287: 28495-28502

  • DOI: 10.1074/jbc.M112.375238
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chiral β-amino acids occur as constituents of various natural and synthetic compounds with potentially useful bioactivities. The pyridoxal 5'-phosphate (PLP)-dependent S-selective transaminase from Mesorhizobium sp. strain LUK (MesAT) is a fold type ...

    Chiral β-amino acids occur as constituents of various natural and synthetic compounds with potentially useful bioactivities. The pyridoxal 5'-phosphate (PLP)-dependent S-selective transaminase from Mesorhizobium sp. strain LUK (MesAT) is a fold type I aminotransferase that can be used for the preparation of enantiopure β-Phe and derivatives thereof. Using x-ray crystallography, we solved structures of MesAT in complex with (S)-β-Phe, (R)-3-amino-5-methylhexanoic acid, 2-oxoglutarate, and the inhibitor 2-aminooxyacetic acid, which allowed us to unveil the molecular basis of the amino acid specificity and enantioselectivity of this enzyme. The binding pocket of the side chain of a β-amino acid is located on the 3'-oxygen side of the PLP cofactor. The same binding pocket is utilized by MesAT to bind the α-carboxylate group of an α-amino acid. A β-amino acid thus binds in a reverse orientation in the active site of MesAT compared with an α-amino acid. Such a binding mode has not been reported before for any PLP-dependent aminotransferase and shows that the active site of MesAT has specifically evolved to accommodate both β- and α-amino acids.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-transaminase
A, B, C
465Mesorhizobium sp. LUKMutation(s): 0 
Find proteins for A3EYF7 (Mesorhizobium sp. LUK)
Go to UniProtKB:  A3EYF7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PLK
Query on PLK

Download SDF File 
Download CCD File 
A, B, C
(3R)-3-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-5-METHYLHEXANOIC ACID
R-3-amino-5-methylhexanoicacid-pyridoxal-5p-phosphate
C15 H25 N2 O7 P
YMKBKDGGJWGJOL-GFCCVEGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.387α = 90.00
b = 94.864β = 113.77
c = 102.973γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2012-07-11
    Type: Other
  • Version 1.2: 2012-08-29
    Type: Database references
  • Version 1.3: 2018-12-05
    Type: Data collection, Database references, Source and taxonomy, Structure summary