2YPO

3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with phenylalanine bound in only one site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Three Sites and You are Out: Ternary Synergistic Allostery Controls Aromatic Aminoacid Biosynthesis in Mycobacterium Tuberculosis.

Blackmore, N.J.Reichau, S.Jiao, W.Hutton, R.D.Baker, E.N.Jameson, G.B.Parker, E.J.

(2013) J Mol Biol 425: 1582

  • DOI: https://doi.org/10.1016/j.jmb.2012.12.019
  • Primary Citation of Related Structures:  
    2YPO, 2YPP, 2YPQ

  • PubMed Abstract: 

    3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyzes the first step in the shikimate pathway, the pathway responsible for the biosynthesis of the aromatic amino acids Trp, Phe, and Tyr. Unlike many other organisms that produce up to three isozymes, each feedback-regulated by one of the aromatic amino acid pathway end products, Mycobacterium tuberculosis expresses a single DAH7PS enzyme that can be controlled by combinations of aromatic amino acids. This study shows that the synergistic inhibition of this enzyme by a combination of Trp and Phe can be significantly augmented by the addition of Tyr. We used X-ray crystallography, mutagenesis, and isothermal titration calorimetry studies to show that DAH7PS from M. tuberculosis possesses a Tyr-selective site in addition to the Trp and Phe sites, revealing an unusual and highly sophisticated network of three synergistic allosteric sites on one enzyme. This ternary inhibitory response, by a combination of all three aromatic amino acids, allows a tunable response of the protein to changing metabolic demands.


  • Organizational Affiliation

    Biomolecular Interaction Centre, Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG
A, B
462Mycobacterium tuberculosisMutation(s): 0 
EC: 2.5.1.54
UniProt
Find proteins for O53512 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53512 
Go to UniProtKB:  O53512
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53512
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth B]
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth A],
K [auth B],
L [auth B],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth A]
M [auth B]
N [auth B]
E [auth A],
F [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PHE PDBBind:  2YPO Kd: 2.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.969α = 90
b = 203.969β = 90
c = 66.6γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references, Refinement description
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description