4CE5

First crystal structure of an (R)-selective omega-transaminase from Aspergillus terreus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of an (R)-Selective Omega-Transaminase from Aspergillus Terreus

Lyskowski, A.Gruber, C.Steinkellner, G.Schurmann, M.Schwab, H.Gruber, K.Steiner, K.

(2014) Plos One 9: 87350

  • DOI: 10.1371/journal.pone.0087350

  • PubMed Abstract: 
  • Chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-Transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a ...

    Chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-Transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (PLP) as cofactor. In nature, (S)-selective amine transaminases are more abundant than the (R)-selective enzymes, and therefore more information concerning their structures is available. Here, we present the crystal structure of an (R)-ω-transaminase from Aspergillus terreus determined by X-ray crystallography at a resolution of 1.6 Å. The structure of the protein is a homodimer that displays the typical class IV fold of PLP-dependent aminotransferases. The PLP-cofactor observed in the structure is present in two states (i) covalently bound to the active site lysine (the internal aldimine form) and (ii) as substrate/product adduct (the external aldimine form) and free lysine. Docking studies revealed that (R)-transaminases follow a dual binding mode, in which the large binding pocket can harbour the bulky substituent of the amine or ketone substrate and the α-carboxylate of pyruvate or amino acids, and the small binding pocket accommodates the smaller substituent.


    Organizational Affiliation

    ACIB GmbH, c/o TU Graz, Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AT-OMEGATA
A, B
333Aspergillus terreus (strain NIH 2624 / FGSC A1156)Mutation(s): 0 
Find proteins for Q0C8G1 (Aspergillus terreus (strain NIH 2624 / FGSC A1156))
Go to UniProtKB:  Q0C8G1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PDG
Query on PDG

Download SDF File 
Download CCD File 
A, B
N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID
N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE
C13 H19 N2 O9 P
JMRKOGDJNHPMHS-SNVBAGLBSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.137 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 105.670α = 90.00
b = 135.310β = 90.00
c = 116.410γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-12
    Type: Initial release