6HX7

Crystal structure of human R180T variant of ORNITHINE AMINOTRANSFERASE at 1.8 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

R180T variant of delta-ornithine aminotransferase associated with gyrate atrophy: biochemical, computational, X-ray and NMR studies provide insight into its catalytic features.

Montioli, R.Paiardini, A.Giardina, G.Zanzoni, S.Cutruzzola, F.Cellini, B.Borri Voltattorni, C.

(2019) FEBS J 286: 2787-2798

  • DOI: https://doi.org/10.1111/febs.14843
  • Primary Citation of Related Structures:  
    6HX7

  • PubMed Abstract: 

    Among the over 50 gyrate atrophy-causing mutations of ornithine δ-aminotransferase (OAT), the R180T involves an active site residue located at the dimer interface, which in the crystal structure of OAT complexed with 5-fluoromethylornithine engages a salt bridge with the α-carboxylate of the substrate analogue. Starting from the previous finding that no transaminase activity was detected in CHO-K 1 cells expressing the R180T variant, here we try to shed light at the protein level on the structural and/or functional defects of the R180T variant. To this aim, the variant has been cloned, expressed, purified and characterized by a combination of biochemical and structural studies. Although the R180T variant shares a similar overall conformation with the wild-type, its crystal structure solved at 1.8 Ǻ reveals slight structural alterations at the active site and at the dimeric interface. These changes are consistent with the spectroscopic and kinetic results, indicating that the variant, as compared with the wild-type OAT, shows (a) an increased K m value for l-ornithine (l-Orn), (b) an altered pyridoxal 5'-phosphate binding mode and affinity and (c) an increased thermostability. In addition, the R180T mutant exhibits a remarkable loss of catalytic activity and is endowed with the ability to catalyse not only the δ-transamination but also, albeit to a lesser extent, the α-transamination of l-Orn. Overall, these data indicate that the slight structural changes caused by the R180T mutation, preventing a proper collocation of l-Orn at the active site of OAT, are responsible for the notable reduction of the catalytic efficiency. ENZYMES: Ornithine aminotransferase EC 2.6.1.13. DATABASES: 6HX7.pdb.


  • Organizational Affiliation

    Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine aminotransferase, mitochondrial
A, B, C
415Homo sapiensMutation(s): 1 
Gene Names: OAT
EC: 2.6.1.13
UniProt & NIH Common Fund Data Resources
Find proteins for P04181 (Homo sapiens)
Explore P04181 
Go to UniProtKB:  P04181
PHAROS:  P04181
GTEx:  ENSG00000065154 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04181
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.252α = 90
b = 193.252β = 90
c = 57.211γ = 120
Software Package:
Software NamePurpose
XDSdata 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
Other privateItalyTelethon Grant GGP15114 to B. Cellini
European Communitys Seventh Framework ProgrammeItalygrant agreement n. 312284

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-15
    Changes: Advisory, Derived calculations
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description