8PNY

Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens complexed with phenylhydrazine and in its apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens.

Shilova, S.A.Matyuta, I.O.Petrova, E.S.Nikolaeva, A.Y.Rakitina, T.V.Minyaev, M.E.Boyko, K.M.Popov, V.O.Bezsudnova, E.Y.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms242216194
  • Primary Citation of Related Structures:  
    8PNW, 8PNY

  • PubMed Abstract: 

    Enzymes with expanded substrate specificity are good starting points for the design of biocatalysts for target reactions. However, the structural basis of the expanded substrate specificity is still elusive, especially in the superfamily of pyridoxal-5'-phosphate-dependent transaminases, which are characterized by a conserved organization of both the active site and functional dimer. Here, we analyze the structure-function relationships in a non-canonical D-amino acid transaminase from Blastococcus saxobsidens , which is active towards D-amino acids and primary ( R )-amines. A detailed study of the enzyme includes a kinetic analysis of its substrate scope and a structural analysis of the holoenzyme and its complex with phenylhydrazine-a reversible inhibitor and analogue of ( R )-1-phenylethylamine-a benchmark substrate of ( R )-selective amine transaminases. We suggest that the features of the active site of transaminase from B. saxobsidens , such as the flexibility of the R34 and R96 residues, the lack of bulky residues in the β-turn at the entrance to the active site, and the short O-pocket loop, facilitate the binding of substrates with and without α-carboxylate groups. The proposed structural determinants of the expanded substrate specificity can be used for the design of transaminases for the stereoselective amination of keto compounds.


  • Organizational Affiliation

    Bach Institute of Biochemistry, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase281Blastococcus saxobsidensMutation(s): 0 
Gene Names: BLASA_4517
UniProt
Find proteins for H6RQF3 (Blastococcus saxobsidens (strain DD2))
Explore H6RQF3 
Go to UniProtKB:  H6RQF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6RQF3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZXN (Subject of Investigation/LOI)
Query on ZXN

Download Ideal Coordinates CCD File 
B [auth A][6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen phosphate
C14 H16 N3 O5 P
VZZGBIJWEDOPQL-LZYBPNLTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.644α = 90
b = 104.644β = 90
c = 51.541γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
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: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references
  • Version 2.0: 2023-12-13
    Changes: Data collection, Database references, Non-polymer description, Structure summary