8ONL

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

Starting Model: experimental
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Literature

In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.

Shilova, S.A.Matyuta, I.O.Khrenova, M.G.Nikolaeva, A.Y.Klyachko, N.L.Minyaev, M.E.Khomutov, A.R.Boyko, K.M.Popov, V.O.Bezsudnova, E.Y.

(2023) Biochem J 480: 1267-1284

  • DOI: https://doi.org/10.1042/BCJ20230233
  • Primary Citation of Related Structures:  
    8AYJ, 8ONJ, 8ONL, 8ONN

  • PubMed Abstract: 

    The development of biocatalysts requires reorganization of the enzyme's active site to facilitate the productive binding of the target substrate and improve turnover number at desired conditions. Pyridoxal-5'-phosphate (PLP) - dependent transaminases are highly efficient biocatalysts for asymmetric amination of ketones and keto acids. However, transaminases, being stereoselective enzymes, have a narrow substrate specificity due to the ordered structure of the active site and work only in neutral-alkaline media. Here, we investigated the d-amino acid transaminase from Aminobacterium colombiense, with the active site organized differently from that of the canonical d-amino acid transaminase from Bacillus sp. YM-1. Using a combination of site-directed mutagenesis, kinetic analysis, molecular modeling, and structural analysis we determined the active site residues responsible for substrate binding, substrate differentiation, thermostability of a functional dimer, and affecting the pH optimum. We demonstrated that the high specificity toward d-glutamate/α-ketoglutarate is due to the interactions of a γ-carboxylate group with K237 residue, while binding of other substrates stems from the effectiveness of their accommodation in the active site optimized for d-glutamate/α-ketoglutarate binding. Furthermore, we showed that the K237A substitution shifts the catalytic activity optimum to acidic pH. Our findings are useful for achieving target substrate specificity and demonstrate the potential for developing and optimizing transaminases for various applications.


  • Organizational Affiliation

    Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase class IV
A, B
277Aminobacterium colombienseMutation(s): 1 
Gene Names: Amico_1844
UniProt
Find proteins for D5EHC5 (Aminobacterium colombiense (strain DSM 12261 / ALA-1))
Explore D5EHC5 
Go to UniProtKB:  D5EHC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5EHC5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.429α = 90
b = 88.013β = 90
c = 99.772γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation19-14-00164

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release