1N8F

Crystal structure of E24Q mutant of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Escherichia Coli in complex with Mn2+ and PEP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 

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Literature

The High-Resolution Structure of 3-Deoxy-D-arabino-heptulosonate-7-phosphate Synthase Reveals a Twist in the Plane of Bound Phosphoenolpyruvate

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

(2003) Biochemistry 42: 3766-3776

  • DOI: 10.1021/bi027257p
  • Primary Citation of Related Structures:  
    1N8F

  • 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 (PEP) and D-erythrose 4-phosphate (E4P) with the formation of DAHP ...

    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 (PEP) and D-erythrose 4-phosphate (E4P) with the formation of DAHP. The native and the selenomethionine-substituted forms of the phenylalanine-regulated isozyme [DAHPS(Phe)] from Escherichia coli were crystallized in complex with PEP and a metal cofactor, Mn(2+), but the crystals displayed disorder in their unit cells, preventing satisfactory refinement. However, the crystal structure of the E24Q mutant form of DAHPS(Phe) in complex with PEP and Mn(2+) has been determined at 1.75 A resolution. Unlike the tetrameric wild-type enzyme, the E24Q enzyme is dimeric in solution, as a result of the mutational perturbation of four intersubunit salt bridges that are critical for tetramer formation. The protein chain conformation and subunit arrangement in the crystals of E24Q and wild-type DAHPS are very similar. However, the interaction of Mn(2+) and PEP in the enzymatically active E24Q mutant complex differs from the Pb(2+)-PEP and Mn(2+)-phosphoglycolate interactions in two enzymatically inactive wild-type complexes whose structures have been determined previously. The geometry of PEP bound in the active site of the E24Q enzyme deviates from planarity due to a 30 degrees twist of the carboxylate plane relative to the enol plane. In addition, seven water molecules are within contact distance of PEP, two of which are close enough to its C2 atom to serve as the nucleophile required in the reaction.


    Organizational Affiliation

    Department of Biology, University of Virginia, Charlottesville, Virginia 22903-2477, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DAHP SynthetaseA, B, C, D350Escherichia coliMutation(s): 1 
Gene Names: aroG
EC: 4.1.2.15 (PDB Primary Data), 2.5.1.54 (UniProt)
UniProt
Find proteins for P0AB91 (Escherichia coli (strain K12))
Explore P0AB91 
Go to UniProtKB:  P0AB91
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEP (Subject of Investigation/LOI)
Query on PEP

Download Ideal Coordinates CCD File 
H [auth A], L [auth B], P [auth C], T [auth D]PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], M [auth C], Q [auth D]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.224α = 90
b = 53.277β = 116.9
c = 150.245γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
TRUNCATEdata reduction
CNSrefinement
ARPmodel building
HKL-2000data scaling
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations