PDBsum entry 1dy3

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Pyrophosphorylase PDB id
Protein chain
158 a.a. *
_MG ×2
Waters ×141
* Residue conservation analysis
PDB id:
Name: Pyrophosphorylase
Title: Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from escherichia coli with atp and a substrate analogue.
Structure: 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase. Chain: a. Synonym: pppk, hppk. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PDB file)
2.0Å     R-factor:   0.165    
Authors: D.K.Stammers,A.Achari,D.O.Somers,P.K.Bryant,J.Rosemond, D.L.Scott,J.N.Champness
Key ref: D.K.Stammers et al. (1999). 2.0 A X-ray structure of the ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue. FEBS Lett, 456, 49-53. PubMed id: 10452528
21-Jan-00     Release date:   18-Aug-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P26281  (HPPK_ECOLI) -  2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
159 a.a.
158 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   4 terms 
  Biochemical function     nucleotide binding     6 terms  


FEBS Lett 456:49-53 (1999)
PubMed id: 10452528  
2.0 A X-ray structure of the ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.
D.K.Stammers, A.Achari, D.O.Somers, P.K.Bryant, J.Rosemond, D.L.Scott, J.N.Champness.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21152407 C.W.Pemble, P.K.Mehta, S.Mehra, Z.Li, A.Nourse, R.E.Lee, and S.W.White (2010).
Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase•dihydropteroate synthase bifunctional enzyme from Francisella tularensis.
  PLoS One, 5, e14165.
PDB codes: 3mcm 3mcn 3mco
16997145 A.Nzila (2006).
Inhibitors of de novo folate enzymes in Plasmodium falciparum.
  Drug Discov Today, 11, 939-944.  
15821168 R.Yang, M.C.Lee, H.Yan, and Y.Duan (2005).
Loop conformation and dynamics of the Escherichia coli HPPK apo-enzyme and its binary complex with MgATP.
  Biophys J, 89, 95.  
15372084 M.B.Schmid (2004).
Seeing is believing: the impact of structural genomics on antimicrobial drug discovery.
  Nat Rev Microbiol, 2, 739-746.  
12111724 A.Bermingham, and J.P.Derrick (2002).
The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery.
  Bioessays, 24, 637-648.  
  11546767 B.Xiao, G.Shi, J.Gao, J.Blaszczyk, Q.Liu, X.Ji, and H.Yan (2001).
Unusual conformational changes in 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as revealed by X-ray crystallography and NMR.
  J Biol Chem, 276, 40274-40281.
PDB codes: 1eq0 1eqm
11435118 L.J.Baker, J.A.Dorocke, R.A.Harris, and D.E.Timm (2001).
The crystal structure of yeast thiamin pyrophosphokinase.
  Structure, 9, 539-546.
PDB code: 1ig0
11080626 J.Blaszczyk, G.Shi, H.Yan, and X.Ji (2000).
Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution.
  Structure, 8, 1049-1058.
PDB codes: 1eqo 1q0n
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