spacer
spacer

PDBsum entry 1rao

Go to PDB code: 
protein ligands links
Transferase PDB id
1rao
Jmol
Contents
Protein chain
158 a.a. *
Ligands
AMP
HH2
Waters ×240
* Residue conservation analysis
PDB id:
1rao
Name: Transferase
Title: Crystal structure of a ternary complex of e. Coli hppk with amp and 6-hydroxymethylpterin-diphosphate at 1.56 angstrom resolution
Structure: 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase. Chain: a. Synonym: 7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase, hppk, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, pppk. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: folk, b0142. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.56Å     R-factor:   0.150     R-free:   0.188
Authors: J.Blaszczyk,X.Ji
Key ref:
J.Blaszczyk et al. (2004). Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Structure, 12, 467-475. PubMed id: 15016362 DOI: 10.1016/j.str.2004.02.003
Date:
31-Oct-03     Release date:   09-Nov-04    
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

 Enzyme reactions 
   Enzyme class: E.C.2.7.6.3  - 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Folate Biosynthesis (late stages)
      Reaction: ATP + 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine = AMP + (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate
ATP
+
2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine
Bound ligand (Het Group name = HH2)
matches with 63.00% similarity
=
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly
+ (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   4 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2004.02.003 Structure 12:467-475 (2004)
PubMed id: 15016362  
 
 
Reaction trajectory of pyrophosphoryl transfer catalyzed by 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
J.Blaszczyk, G.Shi, Y.Li, H.Yan, X.Ji.
 
  ABSTRACT  
 
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the Mg(2+)-dependent pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The reaction follows a bi-bi mechanism with ATP as the first substrate and AMP and HP pyrophosphate (HPPP) as the two products. HPPK is a key enzyme in the folate biosynthetic pathway and is essential for microorganisms but absent from mammals. For the HPPK-catalyzed pyrophosphoryl transfer, a reaction coordinate is constructed on the basis of the thermodynamic and transient kinetic data we reported previously, and the reaction trajectory is mapped out with five three-dimensional structures of the enzyme at various liganded states. The five structures are apo-HPPK (ligand-free enzyme), HPPK.MgATP(analog) (binary complex of HPPK with its first substrate) and HPPK.MgATP(analog).HP (ternary complex of HPPK with both substrates), which we reported previously, and HPPK.AMP.HPPP (ternary complex of HPPK with both product molecules) and HPPK.HPPP (binary complex of HPPK with one product), which we present in this study.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Reaction Coordinate of HPPK-Catalyzed Pyrophosphoryl TransferSix distinct states are proposed along the reaction coordinate, including apo-HPPK, HPPK·MgATP, HPPK·MgATP·HP, HPPK·MgAMP-PP-HP, HPPK·MgAMP·HPPP, and HPPK·HPPP. For each catalytic state, a snapshot is provided with either a three-dimensional structure or a model, including (A and G) the crystal structure of apo-HPPK (Xiao et al., 1999), (B) the NMR solution structure of HPPK·MgAMPPCP (Xiao et al., 2001) mimicking HPPK·MgATP, (C) the crystal structure of HPPK·MgAMPCPP·HP (Blaszczyk et al., 2000) mimicking HPPK·MgATP·HP, (D) the model of HPPK·MgAMP-PP-HP (this work), (E) the crystal structure of HPPK·AMP·HPPP (this work), and (F) the crystal structure of HPPK·HPPP (this work). Helices are illustrated as cyan spirals, strands as orange arrows, and loops as gray pipes except that loop 3 is highlighted in red. The side chain of W89 is shown as a ball-and-stick model and the ligands as van der Waals spheres (Mg2+ ion in black, AMPCPP and AMP in yellow, HP and HPPP in green, and PP in purple). The relative energies of the various states should not be inferred from the diagram.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 467-475) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18007032 J.Blaszczyk, Y.Li, S.Cherry, J.Alexandratos, Y.Wu, G.Shaw, J.E.Tropea, D.S.Waugh, H.Yan, and X.Ji (2007).
Structure and activity of Yersinia pestis 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase as a novel target for the development of antiplague therapeutics.
  Acta Crystallogr D Biol Crystallogr, 63, 1169-1177.
PDB code: 2qx0
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 code is shown on the right.