Crystal structure of a novel thermostable (S)-enantioselective omega-transaminase from Thermomicrobium roseum

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.171 

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Structural basis of substrate recognition by a novel thermostable (S)-enantioselective omega-transaminase from Thermomicrobium roseum.

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

(2019) Sci Rep 9: 6958-6958

  • DOI: https://doi.org/10.1038/s41598-019-43490-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Transaminases catalyze the reversible transfer reaction of an amino group between a primary amine and an α-keto acid, utilizing pyridoxal 5'-phosphate as a cofactor. ω-transaminases (ωTAs) recognize an amino group linked to a non-α carbon of amine substrates. Recently, a novel (S)-enantioselective ωTA from Thermomicrobium roseum (Tr-ωTA) was identified and its enzymatic activity reported. However, the detailed mechanism of (S)-enantioselective substrate recognition remained unclear. In this study, we determined the crystal structure of Tr-ωTA at 1.8 Å resolution to elucidate the mechanism underlying Tr-ωTA substrate (S)-enantioselectivity. A structural analysis of Tr-ωTA along with molecular docking simulations revealed that two pockets at the active site tightly restrict the size and orientation of functional groups of substrate candidates. Based on the structural information and docking simulation results, we propose a comprehensive catalytic mechanism of Tr-ωTA. The present study thus provides structural and functional insights into the (S)-enantioselectivity of Tr-ωTA.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase, class III
A, B
451Thermomicrobium roseum DSM 5159Mutation(s): 0 
Gene Names: trd_1080
Find proteins for B9L0K9 (Thermomicrobium roseum (strain ATCC 27502 / DSM 5159 / P-2))
Explore B9L0K9 
Go to UniProtKB:  B9L0K9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9L0K9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMP (Subject of Investigation/LOI)
Query on PMP

Download Ideal Coordinates CCD File 
C8 H13 N2 O5 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.171 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.258α = 90
b = 118.258β = 90
c = 170.514γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

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: 2019-05-22
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description