6XU3 | pdb_00006xu3

(R)-selective amine transaminase from Shinella sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (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 PLGClick on this verticalbar to view detailsBest 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
Class IV aminotransferase
A, B, C, D
328Shinella sp. JR1-6Mutation(s): 0 
Gene Names: EXZ48_21850
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLG
Query on PLG

Download Ideal Coordinates CCD File 
J [auth B],
N [auth C]
N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
C10 H15 N2 O7 P
FEVQWBMNLWUBTF-UHFFFAOYSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
T [auth D]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
GAB
Query on GAB

Download Ideal Coordinates CCD File 
K [auth B]3-AMINOBENZOIC ACID
C7 H7 N O2
XFDUHJPVQKIXHO-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
P [auth C],
Q [auth C],
U [auth D],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
H [auth A]
L [auth B]
M [auth B]
R [auth C]
S [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.374α = 90
b = 82.118β = 90
c = 222.435γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

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 PLGClick on this verticalbar to view detailsBest 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