Arabidopsis thaliana prephenate aminotransferase

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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This is version 1.3 of the entry. See complete history


Structural basis for substrate recognition and inhibition of prephenate aminotransferase from Arabidopsis.

Holland, C.K.Berkovich, D.A.Kohn, M.L.Maeda, H.Jez, J.M.

(2018) Plant J 94: 304-314

  • DOI: https://doi.org/10.1111/tpj.13856
  • Primary Citation of Related Structures:  
    5WMH, 5WMI, 5WMK, 5WML

  • PubMed Abstract: 

    Aromatic amino acids are protein building blocks and precursors to a number of plant natural products, such as the structural polymer lignin and a variety of medicinally relevant compounds. Plants make tyrosine and phenylalanine by a different pathway from many microbes; this pathway requires prephenate aminotransferase (PAT) as the key enzyme. Prephenate aminotransferase produces arogenate, the unique and immediate precursor for both tyrosine and phenylalanine in plants, and also has aspartate aminotransferase (AAT) activity. The molecular mechanisms governing the substrate specificity and activation or inhibition of PAT are currently unknown. Here we present the X-ray crystal structures of the wild-type and various mutants of PAT from Arabidopsis thaliana (AtPAT). Steady-state kinetic and ligand-binding analyses identified key residues, such as Glu108, that are involved in both keto acid and amino acid substrate specificities and probably contributed to the evolution of PAT activity among class Ib AAT enzymes. Structures of AtPAT mutants co-crystallized with either α-ketoglutarate or pyridoxamine 5'-phosphate and glutamate further define the molecular mechanisms underlying recognition of keto acid and amino acid substrates. Furthermore, cysteine was identified as an inhibitor of PAT from A. thaliana and Antirrhinum majus plants as well as the bacterium Chlorobium tepidum, uncovering a potential new effector of PAT.

  • Organizational Affiliation

    Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase
A, B, C, D, E
A, B, C, D, E, F
475Arabidopsis thalianaMutation(s): 0 
Gene Names: PATAATMEE17At2g22250T26C19.9
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
Find proteins for Q9SIE1 (Arabidopsis thaliana)
Explore Q9SIE1 
Go to UniProtKB:  Q9SIE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SIE1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.343α = 90
b = 111.575β = 90.37
c = 141.775γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
SCALEPACKdata scaling
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB--1157771

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description