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PDBsum entry 1dy3

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protein ligands metals links
Pyrophosphorylase PDB id
1dy3
Jmol
Contents
Protein chain
158 a.a. *
Ligands
ATP
87Y
Metals
_MG ×2
Waters ×141
* Residue conservation analysis
PDB id:
1dy3
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)
Resolution:
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
Date:
21-Jan-00     Release date:   18-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26281  (HPPK_ECOLI) -  2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Seq:
Struc:
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.
 
  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.
 

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
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.