6F77

Crystal structure of the prephenate aminotransferase from Rhizobium meliloti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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This is version 1.1 of the entry. See complete history


Literature

Tyrosine metabolism: identification of a key residue in the acquisition of prephenate aminotransferase activity by 1 beta aspartate aminotransferase.

Giustini, C.Graindorge, M.Cobessi, D.Crouzy, S.Robin, A.Curien, G.Matringe, M.

(2019) FEBS J 286: 2118-2134

  • DOI: 10.1111/febs.14789
  • Primary Citation of Related Structures:  
    6F35, 6F5V, 6F77

  • PubMed Abstract: 
  • Alternative routes for the post-chorismate branch of the biosynthetic pathway leading to tyrosine exist, the 4-hydroxyphenylpyruvate or the arogenate route. The arogenate route involves the transamination of prephenate into arogenate. In a previous study, we found that, depending on the microorganisms possessing the arogenate route, three different aminotransferases evolved to perform prephenate transamination, that is, 1β aspartate aminotransferase (1β AAT), N-succinyl-l,l-diaminopimelate aminotransferase, and branched-chain aminotransferase ...

    Alternative routes for the post-chorismate branch of the biosynthetic pathway leading to tyrosine exist, the 4-hydroxyphenylpyruvate or the arogenate route. The arogenate route involves the transamination of prephenate into arogenate. In a previous study, we found that, depending on the microorganisms possessing the arogenate route, three different aminotransferases evolved to perform prephenate transamination, that is, 1β aspartate aminotransferase (1β AAT), N-succinyl-l,l-diaminopimelate aminotransferase, and branched-chain aminotransferase. The present work aimed at identifying molecular determinant(s) of 1β AAT prephenate aminotransferase (PAT) activity. To that purpose, we conducted X-ray crystal structure analysis of two PAT competent 1β AAT from Arabidopsis thaliana and Rhizobium meliloti and one PAT incompetent 1β AAT from R. meliloti. This structural analysis supported by site-directed mutagenesis, modeling, and molecular dynamics simulations allowed us to identify a molecular determinant of PAT activity in the flexible N-terminal loop of 1β AAT. Our data reveal that a Lys/Arg/Gln residue in position 12 in the sequence (numbering according to Thermus thermophilus 1β AAT), present only in PAT competent enzymes, could interact with the 4-hydroxyl group of the prephenate substrate, and thus may have a central role in the acquisition of PAT activity by 1β AAT.


    Organizational Affiliation

    INRA, CNRS, CEA, BIG-LPCV, University of Grenoble Alpes, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate aminotransferase AA, C, D, E, F400Sinorhizobium meliloti 1021Mutation(s): 0 
Gene Names: aatAR02325SMc01578
EC: 2.6.1.1 (PDB Primary Data), 2.6.1.79 (UniProt)
UniProt
Find proteins for Q02635 (Rhizobium meliloti (strain 1021))
Explore Q02635 
Go to UniProtKB:  Q02635
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate aminotransferase AB400Sinorhizobium meliloti 1021Mutation(s): 0 
Gene Names: aatAR02325SMc01578
EC: 2.6.1.1 (PDB Primary Data), 2.6.1.79 (UniProt)
UniProt
Find proteins for Q02635 (Rhizobium meliloti (strain 1021))
Explore Q02635 
Go to UniProtKB:  Q02635
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
BL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.543α = 90
b = 93.008β = 91.36
c = 123.069γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references