5WMH

Arabidopsis thaliana prephenate aminotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

  • 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 pathwa ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferaseABCDEF475Arabidopsis thalianaMutation(s): 0 
Gene Names: PATAATMEE17At2g22250T26C19.9
EC: 2.6.1.1 (PDB Primary Data), 2.6.1.78 (PDB Primary Data), 2.6.1.79 (PDB Primary Data)
Find proteins for Q9SIE1 (Arabidopsis thaliana)
Explore Q9SIE1 
Go to UniProtKB:  Q9SIE1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B, C, D, E, F
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-3000data collection
PHASERphasing
SCALEPACKdata scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • 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