5J6F

Crystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate.

Nazmi, A.R.Lang, E.J.M.Bai, Y.Allison, T.M.Othman, M.H.Panjikar, S.Arcus, V.L.Parker, E.J.

(2016) J Biol Chem 291: 21836-21847

  • DOI: 10.1074/jbc.M116.741637
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Multifunctional proteins play a variety of roles in metabolism. Here, we examine the catalytic function of the combined 3-deoxy-d- arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM) from Geobacillus sp. DA ...

    Multifunctional proteins play a variety of roles in metabolism. Here, we examine the catalytic function of the combined 3-deoxy-d- arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM) from Geobacillus sp. DAH7PS operates at the start of the biosynthetic pathway for aromatic metabolites, whereas CM operates in a dedicated branch of the pathway for the biosynthesis of amino acids tyrosine and phenylalanine. In line with sequence predictions, the two catalytic functions are located in distinct domains, and these two activities can be separated and retain functionality. For the full-length protein, prephenate, the product of the CM reaction, acts as an allosteric inhibitor for the DAH7PS. The crystal structure of the full-length protein with prephenate bound and the accompanying small angle x-ray scattering data reveal the molecular mechanism of the allostery. Prephenate binding results in the tighter association between the dimeric CM domains and the tetrameric DAH7PS, occluding the active site and therefore disrupting DAH7PS function. Acquisition of a physical gating mechanism to control catalytic function through gene fusion appears to be a general mechanism for providing allostery for this enzyme.


    Organizational Affiliation

    the Maurice Wilkins Centre, Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, P. O. Box 4800, Christchurch 8140, New Zealand emily.parker@canterbury.ac.nz.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
A, B
368Geobacillus sp. GHH01Mutation(s): 0 
Gene Names: aroAGHH_c28860
EC: 2.5.1.54 (PDB Primary Data), 5.4.99.5 (PDB Primary Data)
Find proteins for L8A208 (Geobacillus sp. GHH01)
Go to UniProtKB:  L8A208
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRE
Query on PRE

Download CCD File 
A, B
PREPHENIC ACID
C10 H10 O6
FPWMCUPFBRFMLH-XGAOUMNUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.438α = 90
b = 95.438β = 90
c = 167.452γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Database references, Derived calculations