Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (holo form).

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

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The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis : Biochemical and Structural Insights into the New Enzyme.

Bakunova, A.K.Nikolaeva, A.Y.Rakitina, T.V.Isaikina, T.Y.Khrenova, M.G.Boyko, K.M.Popov, V.O.Bezsudnova, E.Y.

(2021) Molecules 26

  • DOI: https://doi.org/10.3390/molecules26165053

  • PubMed Abstract: 

    Among industrially important pyridoxal-5'-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

  • Organizational Affiliation

    Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase class IV301Haliscomenobacter hydrossis DSM 1100Mutation(s): 0 
Gene Names: Halhy_2446
Find proteins for F4KWH0 (Haliscomenobacter hydrossis (strain ATCC 27775 / DSM 1100 / LMG 10767 / O))
Explore F4KWH0 
Go to UniProtKB:  F4KWH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4KWH0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.884α = 90
b = 71.752β = 100.96
c = 52.992γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
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: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-10-06
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-10
    Changes: Structure summary
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description