Human Ornithine Aminotransferase (hOAT) soaked with 5-aminovaleric acid

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-12-20 Released: 2022-05-04 
  • Deposition Author(s): Butrin, A., Liu, D.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase.

Butrin, A.Butrin, A.Wawrzak, Z.Moran, G.R.Liu, D.

(2022) J Biol Chem 298: 101969-101969

  • DOI: https://doi.org/10.1016/j.jbc.2022.101969
  • Primary Citation of Related Structures:  
    7T9Z, 7TA0, 7TA1

  • PubMed Abstract: 

    Hepatocellular carcinoma (HCC) is the most common primary cancer of the liver and occurs predominantly in patients with underlying chronic liver diseases. Over the past decade, human ornithine aminotransferase (hOAT), which is an enzyme that catalyzes the metabolic conversion of ornithine into an intermediate for proline or glutamate synthesis, has been found to be overexpressed in HCC cells. hOAT has since emerged as a promising target for novel anticancer therapies, especially for the ongoing rational design effort to discover mechanism-based inactivators (MBIs). Despite the significance of hOAT in human metabolism and its clinical potential as a drug target against HCC, there are significant knowledge deficits with regard to its catalytic mechanism and structural characteristics. Ongoing MBI design efforts require in-depth knowledge of the enzyme active site, in particular, pKa values of potential nucleophiles and residues necessary for the molecular recognition of ligands. Here, we conducted a study detailing the fundamental active-site properties of hOAT using stopped-flow spectrophotometry and X-ray crystallography. Our results quantitatively revealed the pH dependence of the multistep reaction mechanism and illuminated the roles of ornithine α-amino and δ-amino groups in substrate recognition and in facilitating catalytic turnover. These findings provided insights of the catalytic mechanism that could benefit the rational design of MBIs against hOAT. In addition, substrate recognition and turnover of several fragment-sized alternative substrates of hOATs, which could serve as structural templates for MBI design, were also elucidated.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine aminotransferase, mitochondrial
A, B, C
439Homo 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
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.906α = 90
b = 114.906β = 90
c = 185.181γ = 120
Software Package:
Software NamePurpose
autoPROCdata reduction
pointlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1R01CA260250-01

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description