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

Validation slider image for 6XU3

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 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.

Macromolecule Content 

  • Total Structure Weight: 149.19 kDa 
  • Atom Count: 11,032 
  • Modeled Residue Count: 1,285 
  • Deposited Residue Count: 1,312 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

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]
H [auth A],
L [auth B],
M [auth B],
R [auth C],
S [auth C],
W [auth D]
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 


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