6SNL

(R)-selective amine transaminase from Exophiala sideris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Expanding the Toolbox of R-Selective Amine Transaminases by Identification and Characterization of New Members.

Telzerow, A.Paris, J.Hakansson, M.Gonzalez-Sabin, J.Rios-Lombardia, N.Groger, H.Moris, F.Schurmann, M.Schwab, H.Steiner, K.

(2021) Chembiochem 22: 1232-1242

  • DOI: https://doi.org/10.1002/cbic.202000692
  • Primary Citation of Related Structures:  
    6SNL, 6XU3

  • PubMed Abstract: 

    Amine transaminases (ATAs) are used to synthesize enantiomerically pure amines, which are building blocks for pharmaceuticals and agrochemicals. R-selective ATAs belong to the fold type IV PLP-dependent enzymes, and different sequence-, structure- and substrate scope-based features have been identified in the past decade. However, our knowledge is still restricted due to the limited number of characterized (R)-ATAs, with additional bias towards fungal origin. We aimed to expand the toolbox of (R)-ATAs and contribute to the understanding of this enzyme subfamily. We identified and characterized four new (R)-ATAs. The ATA from Exophiala sideris contains a motif characteristic for d-ATAs, which was previously believed to be a disqualifying factor for (R)-ATA activity. The crystal structure of the ATA from Shinella is the first from a Gram-negative bacterium. The ATAs from Pseudonocardia acaciae and Tetrasphaera japonica are the first characterized (R)-ATAs with a shortened/missing N-terminal helix. The active-site charges vary significantly between the new and known ATAs, correlating with their diverging substrate scope.


  • Organizational Affiliation

    Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
amine transaminase
A, B, C, D, E
A, B, C, D, E, F
347Exophiala siderisMutation(s): 0 
Gene Names: PV11_02554
UniProt
Find proteins for A0A0D1XFW6 (Exophiala sideris)
Explore A0A0D1XFW6 
Go to UniProtKB:  A0A0D1XFW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D1XFW6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
M [auth C]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
N [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
N [auth D],
O [auth E],
P [auth F]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth C],
Q [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.263 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.113α = 90
b = 301.521β = 90
c = 140.657γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionAustria634200

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description