8JHE

Hyper-thermostable ancestral L-amino acid oxidase 2 (HTAncLAAO2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural and functional analysis of hyper-thermostable ancestral L-amino acid oxidase that can convert Trp derivatives to D-forms by chemoenzymatic reaction.

Kawamura, Y.Ishida, C.Miyata, R.Miyata, A.Hayashi, S.Fujinami, D.Ito, S.Nakano, S.

(2023) Commun Chem 6: 200-200

  • DOI: https://doi.org/10.1038/s42004-023-01005-1
  • Primary Citation of Related Structures:  
    8JHE

  • PubMed Abstract: 

    Production of D-amino acids (D-AAs) on a large-scale enables to provide precursors of peptide therapeutics. In this study, we designed a novel L-amino acid oxidase, HTAncLAAO2, by ancestral sequence reconstruction, exhibiting high thermostability and long-term stability. The crystal structure of HTAncLAAO2 was determined at 2.2 Å by X-ray crystallography, revealing that the enzyme has an octameric form like a "ninja-star" feature. Enzymatic property analysis demonstrated that HTAncLAAO2 exhibits three-order larger k cat /K m values towards four L-AAs (L-Phe, L-Leu, L-Met, and L-Ile) than that of L-Trp. Through screening the variants, we obtained the HTAncLAAO2(W220A) variant, which shows a > 6-fold increase in k cat value toward L-Trp compared to the original enzyme. This variant applies to synthesizing enantio-pure D-Trp derivatives from L- or rac-forms at a preparative scale. Given its excellent properties, HTAncLAAO2 would be a starting point for designing novel oxidases with high activity toward various amines and AAs.


  • Organizational Affiliation

    Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hyper thermostable ancestral L-amino acid oxidase
A, B, C, D
555synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.167 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.896α = 90
b = 180.896β = 90
c = 81.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K14391
Japan Society for the Promotion of Science (JSPS)Japan21K05395
Japan Science and TechnologyJapanJPMJPR20AB

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release