8YRV

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis complexed with 3-aminooxypropionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Literature

Insights into the Functioning of the D-amino Acid Transaminase from Haliscomenobacter Hydrossis via a Structural and Spectral Analysis of its Complex with 3-Aminooxypropionic Acid.

Bakunova, A.K.Matyuta, I.O.Nikolaeva, A.Y.Boyko, K.M.Khomutov, A.R.Bezsudnova, E.Y.Popov, V.O.

(2024) Acta Naturae 16: 18-24

  • DOI: https://doi.org/10.32607/actanaturae.27496
  • Primary Citation of Related Structures:  
    8YRV

  • PubMed Abstract: 

    Pyridoxal 5'-phosphate-dependent enzymes play a crucial role in nitrogen metabolism. Carbonyl compounds, such as O-substituted hydroxylamines, stand out among numerous specific inhibitors of these enzymes, including those of practical importance, because they react with pyridoxal 5'-phosphate in the active site of the enzymes to form stable oximes. O-substituted hydroxylamines mimic the side group of amino acid substrates, thus providing highly potent and specific inhibition of the corresponding enzymes. The interaction between D-amino acid transaminase from bacterium Haliscomenobacter hydrossis and 3-aminooxypropionic acid was studied in the present work. The structural and spectral analyses of the complex of this transaminase with 3-aminooxypropionic acid allowed us to clarify some features of the organization and functioning of its active site and illustrate one of the mechanisms of inhibition by the specific substrate, D-glutamic acid.


  • Organizational Affiliation

    Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071 Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase class IV283Haliscomenobacter hydrossis DSM 1100Mutation(s): 0 
Gene Names: Halhy_2446
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OCF (Subject of Investigation/LOI)
Query on OCF

Download Ideal Coordinates CCD File 
B [auth A]3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid
C11 H15 N2 O8 P
WFKOVQOIGDESOJ-WLRTZDKTSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.772α = 90
b = 71.232β = 101.26
c = 52.549γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references, Structure summary