6SNL | pdb_00006snl

(R)-selective amine transaminase from Exophiala sideris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 
    0.289 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLPClick on this verticalbar to view details

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
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]
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 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.263 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PLPClick on this verticalbar to view details

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