1KFL

Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from E.coli complexed with Mn2+, PEP, and Phe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Allosteric inhibition of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase alters the coordination of both substrates.

Shumilin, I.A.Zhao, C.Bauerle, R.Kretsinger, R.H.

(2002) J.Mol.Biol. 320: 1147-1156


  • PubMed Abstract: 
  • 3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS), the first enzyme of the aromatic biosynthetic pathway in microorganisms and plants, catalyzes the aldol-like condensation of phosphoenolpyruvate and D-erythrose-4-phosphate with the format ...

    3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS), the first enzyme of the aromatic biosynthetic pathway in microorganisms and plants, catalyzes the aldol-like condensation of phosphoenolpyruvate and D-erythrose-4-phosphate with the formation of 3-deoxy-D-arabino-heptulosonate-7-phosphate. In Escherichia coli, there are three isoforms of DAHPS, each specifically feedback-regulated by one of the three aromatic amino acid end products. The crystal structure of the phenylalanine-regulated DAHPS from E.coli in complex with its inhibitor, L-phenylalanine, phosphoenolpyruvate, and metal cofactor, Mn(2+), has been determined to 2.8A resolution. Phe binds in a cavity formed by residues of two adjacent subunits and is located about 20A from the closest active site. A model for the mechanism of allosteric inhibition has been derived from conformational differences between the Phe-bound and previously determined Phe-free structures. Two interrelated paths of conformational changes transmit the inhibitory signal from the Phe-binding site to the active site of DAHPS. The first path involves transmission within a single subunit due to the movement of adjacent segments of the protein. The second involves alterations in the contacts between subunits. The combination of these two paths changes the conformation of one of the active site loops significantly and shifts the other slightly. This alters the interaction of DAHPS with both of its substrates. Upon binding of Phe, the enzyme loses the ability to bind D-erythrose-4-phosphate and binds phosphoenolpyruvate in a flipped orientation.


    Organizational Affiliation

    Department of Biology, University of Virginia, Charlottesville, VA 22903, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-deoxy-D-arabino-heptulosonate-7-phosphate synthase
A, B, C, D, E, F, G, H
350Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aroG
EC: 2.5.1.54
Find proteins for P0AB91 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AB91
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PHE
Query on PHE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
PEP
Query on PEP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 290.097α = 90.00
b = 90.097β = 120.77
c = 155.798γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
SCALEPACKdata scaling
CNSphasing
CCP4data scaling
DMmodel building
DENZOdata reduction
CNSrefinement
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance