6K8H

Crystal structure of an omega-transaminase from Sphaerobacter thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural insights into the enzyme specificity of a novel omega-transaminase from the thermophilic bacterium Sphaerobacter thermophilus.

Kwon, S.Lee, J.H.Kim, C.M.Ha, H.J.Lee, S.H.Lee, C.S.Jeon, J.H.So, I.Park, H.H.

(2019) J Struct Biol 208: 107395-107395

  • DOI: https://doi.org/10.1016/j.jsb.2019.09.012
  • Primary Citation of Related Structures:  
    6K8H

  • PubMed Abstract: 

    Transaminases are pyridoxal 5'-phosphate-dependent enzymes that reversibly catalyze transamination reactions from an amino group donor substrate to an amino group acceptor substrate. ω-Transaminases (ωTAs) utilize compounds with an amino group not at α-carbon position as their amino group donor substrates. Recently, a novel ωTA with broad substrate specificity and high thermostability from the thermophilic bacterium Sphaerobacter thermophilus (St-ωTA) has been reported. Although St-ωTA has been biochemically characterized, little is known about its determinants of substrate specificity. In the present study, we determined the crystal structure of St-ωTA at 1.9 Å resolution to clarify in detail its mechanism of substrate recognition. The structure of St-ωTA revealed that it has a voluminous active site resulting from the unique spatial arrangement of residues comprising its active site. In addition, our molecular docking simulation results suggest that substrate compounds may bind to active site residues via electrostatic interactions or hydrophobic interactions that can be induced by subtle rearrangements of active site residues. On the basis of these structural analyses, we propose a plausible working model of the enzymatic mechanism of St-ωTA. Our results provide profound structural insights into the substrate specificity of St-ωTA and extend the boundaries of knowledge of TAs.


  • Organizational Affiliation

    College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase class-III
A, B
454Sphaerobacter thermophilus DSM 20745Mutation(s): 0 
Gene Names: Sthe_0848
UniProt
Find proteins for D1C218 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022))
Explore D1C218 
Go to UniProtKB:  D1C218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1C218
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLR (Subject of Investigation/LOI)
Query on PLR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
C8 H12 N O5 P
RBCOYOYDYNXAFA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.064α = 90
b = 61.246β = 90
c = 185.389γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017M3A9D8062960
National Research Foundation (Korea)Korea, Republic OfNRF-2018R1A2B3008541

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references
  • Version 1.2: 2020-03-25
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description