7NEA

Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M3 mutant).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Probing the role of the residues in the active site of the transaminase from Thermobaculum terrenum.

Bezsudnova, E.Y.Nikolaeva, A.Y.Bakunova, A.K.Rakitina, T.V.Suplatov, D.A.Popov, V.O.Boyko, K.M.

(2021) PLoS One 16: e0255098-e0255098

  • DOI: https://doi.org/10.1371/journal.pone.0255098
  • Primary Citation of Related Structures:  
    7NEA, 7NEB

  • PubMed Abstract: 

    Creating biocatalysts for (R)-selective amination effectively is highly desirable in organic synthesis. Despite noticeable progress in the engineering of (R)-amine activity in pyridoxal-5'-phosphate-dependent transaminases of fold type IV, the specialization of the activity is still an intuitive task, as there is poor understanding of sequence-structure-function relationships. In this study, we analyzed this relationship in transaminase from Thermobaculum terrenum, distinguished by expanded substrate specificity and activity in reactions with L-amino acids and (R)-(+)-1-phenylethylamine using α-ketoglutarate and pyruvate as amino acceptors. We performed site-directed mutagenesis to create a panel of the enzyme variants, which differ in the active site residues from the parent enzyme to a putative transaminase specific to (R)-primary amines. The variants were examined in the overall transamination reactions and half-reaction with (R)-(+)-1-phenylethylamine. A structural analysis of the most prominent variants revealed a spatial reorganization in the active sites, which caused changes in activity. Although the specialization to (R)-amine transaminase was not implemented, we succeeded in understanding the role of the particular active site residues in expanding substrate specificity of the enzyme. We showed that the specificity for (R)-(+)-1-phenylethylamine in transaminase from T. terrenum arises without sacrificing the specificity for L-amino acids and α-ketoglutarate and in consensus with it.


  • Organizational Affiliation

    Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Branched-chain-amino-acid aminotransferase316Thermobaculum terrenum ATCC BAA-798Mutation(s): 3 
Gene Names: ilvETter_1720
EC: 2.6.1.42
UniProt
Find proteins for D1CCW1 (Thermobaculum terrenum (strain ATCC BAA-798 / CCMEE 7001 / YNP1))
Explore D1CCW1 
Go to UniProtKB:  D1CCW1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1CCW1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.497α = 90
b = 146.497β = 90
c = 143.776γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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: 2021-07-07
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description