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 
  • R-Value Observed: 0.139 

Starting Model: other
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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: https://doi.org/10.1371/journal.pone.0087350
  • Primary Citation of Related Structures:  
    4CE5

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AT-OMEGATA
A, B
333Aspergillus terreusMutation(s): 0 
EC: 2.6.1.42
UniProt
Find proteins for Q0C8G1 (Aspergillus terreus (strain NIH 2624 / FGSC A1156))
Explore Q0C8G1 
Go to UniProtKB:  Q0C8G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0C8G1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PDG
Query on PDG

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID
C13 H19 N2 O9 P
JMRKOGDJNHPMHS-SNVBAGLBSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.67α = 90
b = 135.31β = 90
c = 116.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description