Human Ornithine Aminotransferase (hOAT) co-crystallized with its inactivator 3-Amino-4-fluorocyclopentenecarboxylic Acid

Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Structural and Mechanistic Basis for the Inactivation of Human Ornithine Aminotransferase by (3 S ,4 S )-3-Amino-4-fluorocyclopentenecarboxylic Acid.

Shen, S.Butrin, A.Beaupre, B.A.Ferreira, G.M.Doubleday, P.F.Grass, D.H.Zhu, W.Kelleher, N.L.Moran, G.R.Liu, D.Silverman, R.B.

(2023) Molecules 28

  • DOI: https://doi.org/10.3390/molecules28031133
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ornithine aminotransferase (OAT) is overexpressed in hepatocellular carcinoma (HCC), and we previously showed that inactivation of OAT inhibits the growth of HCC. Recently, we found that (3 S ,4 S )-3-amino-4-fluorocyclopentenecarboxylic acid ( 5 ) was a potent inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), proceeding by an enamine mechanism. Here we describe our investigations into the activity and mechanism of 5 as an inactivator of human OAT. We have found that 5 exhibits 10-fold less inactivation efficiency ( k inact / K I ) against h OAT than GABA-AT. A comprehensive mechanistic study was carried out to understand its inactivation mechanism with h OAT. p K a and electrostatic potential calculations were performed to further support the notion that the α,β-unsaturated alkene of 5 is critical for enhancing acidity and nucleophilicity of the corresponding intermediates and ultimately responsible for the improved inactivation efficiency of 5 over the corresponding saturated analogue ( 4 ). Intact protein mass spectrometry and the crystal structure complex with h OAT provide evidence to conclude that 5 mainly inactivates h OAT through noncovalent interactions, and that, unlike with GABA-AT, covalent binding with h OAT is a minor component of the total inhibition which is unique relative to other monofluoro-substituted derivatives. Furthermore, based on the results of transient-state measurements and free energy calculations, it is suggested that the α,β-unsaturated carboxylate group of PLP-bound 5 may be directly involved in the inactivation cascade by forming an enolate intermediate. Overall, compound 5 exhibits unusual structural conversions which are catalyzed by specific residues within h OAT, ultimately leading to an enamine mechanism-based inactivation of h OAT through noncovalent interactions and covalent modification.

  • Organizational Affiliation

    Department of Chemistry and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine aminotransferase, mitochondrial
A, B, C
404Homo sapiensMutation(s): 0 
Gene Names: OAT
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X8H (Subject of Investigation/LOI)
Query on X8H

Download Ideal Coordinates CCD File 
E [auth B](1R,3S,4Z)-3-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-4-iminocyclopentane-1-carboxylic acid
C14 H19 N2 O7 P
X8B (Subject of Investigation/LOI)
Query on X8B

Download Ideal Coordinates CCD File 
D [auth A],
F [auth C]
(3E,4E)-4-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-iminocyclopent-1-ene-1-carboxylic acid
C14 H15 N2 O7 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.91 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.17α = 90
b = 110.29β = 103.72
c = 57.12γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
xia2data reduction
Aimlessdata scaling
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-13
    Changes: Source and taxonomy