1DY3

Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.

• PDB DOI: https://doi.org/10.2210/pdb1DY3/pdb

• Classification: PYROPHOSPHORYLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-21 Released: 2000-08-18 
• Deposition Author(s): Stammers, D.K., Achari, A., Somers, D.O., Bryant, P.K., Rosemond, J., Scott, D.L., Champness, J.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.165 

Literature

2.0A X-Ray Structure of the Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase from Escherichia Coli with ATP and a Substrate Analogue

Stammers, D.K., Achari, A., Somers, D.O., Bryant, P.K., Rosemond, J., Scott, D.L., Champness, J.N.

(1999) FEBS Lett 456: 49

• PubMed: 10452528 
• DOI: https://doi.org/10.1016/s0014-5793(99)00860-1
• Primary Citation of Related Structures:  
  1DY3


• PubMed Abstract: 
  

  The X-ray crystal structure of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase (PPPK) in a ternary complex with ATP and a pterin analogue has been solved to 2.0 A resolution, giving, for the first time, detailed information of the PPPK/ATP intermolecular interactions and the accompanying conformational change. The first 100 residues of the 158 residue peptide contain a betaalpha betabeta alphabeta motif present in several other proteins including nucleoside diphosphate kinase. Comparative sequence examination of a wide range of prokaryotic and lower eukaryotic species confirms the conservation of the PPPK active site, indicating the value of this de novo folate biosynthesis pathway enzyme as a potential target for the development of novel broad-spectrum anti-infective agents.

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Organizational Affiliation: 

Glaxo Wellcome R&D, Medicines Research Centre, Stevenage, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 18.84 kDa 
• Atom Count: 1,464 
• Modelled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase	A	158	Escherichia coli	Mutation(s): 0  Gene Names: folK, b0142, JW0138 EC: 2.7.6.3
UniProt
Find proteins for P26281 (Escherichia coli (strain K12)) Explore P26281  Go to UniProtKB:  P26281

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
87Y	C [auth A]	7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN C16 H19 N5 O2 XMFJTCGUDFSWSW-INIZCTEOSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.165 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.96	α = 90
b = 69.01	β = 90
c = 115.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-18 
Deposition Author(s): Stammers, D.K., Achari, A., Somers, D.O., Bryant, P.K., Rosemond, J., Scott, D.L., Champness, J.N.

Revision History  

• Version 1.0: 2000-08-18
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary