5T9F

Prephenate Dehydrogenase N222D mutant from Soybean


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants.

Schenck, C.A.Holland, C.K.Schneider, M.R.Men, Y.Lee, S.G.Jez, J.M.Maeda, H.A.

(2017) Nat Chem Biol 13: 1029-1035

  • DOI: https://doi.org/10.1038/nchembio.2414
  • Primary Citation of Related Structures:  
    5T95, 5T9E, 5T9F, 5WHX

  • PubMed Abstract: 

    L-Tyrosine (Tyr) is essential for protein synthesis and is a precursor of numerous specialized metabolites crucial for plant and human health. Tyr can be synthesized via two alternative routes by different key regulatory TyrA family enzymes, prephenate dehydrogenase (PDH, also known as TyrA p ) or arogenate dehydrogenase (ADH, also known as TyrA a ), representing a unique divergence of primary metabolic pathways. The molecular foundation underlying the evolution of these alternative Tyr pathways is currently unknown. Here we characterized recently diverged plant PDH and ADH enzymes, obtained the X-ray crystal structure of soybean PDH, and identified a single amino acid residue that defines TyrA substrate specificity and regulation. Structures of mutated PDHs co-crystallized with Tyr indicate that substitutions of Asn222 confer ADH activity and Tyr sensitivity. Reciprocal mutagenesis of the corresponding residue in divergent plant ADHs further introduced PDH activity and relaxed Tyr sensitivity, highlighting the critical role of this residue in TyrA substrate specificity that underlies the evolution of alternative Tyr biosynthetic pathways in plants.


  • Organizational Affiliation

    Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prephenate dehydrogenase 1
A, B
271Glycine maxMutation(s): 1 
Gene Names: PDH1GLYMA_18G023100
EC: 1.3.1.13
UniProt
Find proteins for I1MYY4 (Glycine max)
Explore I1MYY4 
Go to UniProtKB:  I1MYY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI1MYY4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.445α = 107.82
b = 55.046β = 99.56
c = 68.387γ = 102.58
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing

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 StatesNSF-MCB--1157771

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2018-04-18
    Changes: Data collection
  • Version 1.5: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.6: 2024-03-06
    Changes: Data collection, Database references