spacer
spacer

PDBsum entry 1q0n

Go to PDB code: 
protein ligands metals links
Transferase PDB id
1q0n
Jmol
Contents
Protein chain
158 a.a. *
Ligands
ACT ×4
APC
PH2
Metals
_MG ×2
_CL
Waters ×343
* Residue conservation analysis
PDB id:
1q0n
Name: Transferase
Title: Crystal structure of a ternary complex of 6-hydroxymethyl-7, 8-dihydropterin pyrophosphokinase from e. Coli with mgampcpp and 6-hydroxymethyl-7,8-dihydropterin at 1.25 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 or b0142. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.25Å     R-factor:   0.115     R-free:   0.147
Authors: J.Blaszczyk,X.Ji
Key ref:
J.Blaszczyk et al. (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. PubMed id: 11080626 DOI: 10.1016/S0969-2126(00)00502-5
Date:
16-Jul-03     Release date:   26-Aug-03    
Supersedes: 1eqo
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 = PH2)
corresponds exactly
=
AMP
Bound ligand (Het Group name = APC)
matches with 68.00% similarity
+ (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/S0969-2126(00)00502-5 Structure 8:1049-1058 (2000)
PubMed id: 11080626  
 
 
Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution.
J.Blaszczyk, G.Shi, H.Yan, X.Ji.
 
  ABSTRACT  
 
BACKGROUND: Folates are essential for life. Unlike mammals, most microorganisms must synthesize folates de novo. 6-Hydroxymethyl-7, 8-dihydropterin pyrophosphokinase (HPPK) catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in the folate pathway, and therefore is an ideal target for developing novel antimicrobial agents. HPPK from Escherichia coli is a 158-residue thermostable protein that provides a convenient model system for mechanistic studies. Crystal structures have been reported for HPPK without bound ligand, containing an HP analog, and complexed with an HP analog, two Mg(2+) ions, and ATP. RESULTS: We present the 1.25 A crystal structure of HPPK in complex with HP, two Mg(2+) ions, and AMPCPP (an ATP analog that inhibits the enzymatic reaction). This structure demonstrates that the enzyme seals the active center where the reaction occurs. The comparison with unligated HPPK reveals dramatic conformational changes of three flexible loops and many sidechains. The coordination of Mg(2+) ions has been defined and the roles of 26 residues have been derived. CONCLUSIONS: HPPK-HP-MgAMPCPP mimics most closely the natural ternary complex of HPPK and provides details of protein-substrate interactions. The coordination of the two Mg(2+) ions helps create the correct geometry for the one-step reaction of pyrophosphoryl transfer, for which we suggest an in-line single displacement mechanism with some associative character in the transition state. The rigidity of the adenine-binding pocket and hydrogen bonds are responsible for adenosine specificity. The nonconserved residues that interact with the substrate might be responsible for the species-dependent properties of an isozyme.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The Open and Closed Catalytic Center of HPPK(a) The three uncoupled flexible loops of HPPK in the apo-enzyme [2].(b) The coupling of these loops in the ternary complex. In the ternary complex, a hydrogen-bond network involves N10 from Loop-1; P47 and Q50 from Loop-2; and W89, P91, and R92 from Loop-3. This network is not observed in apo-HPPK. The orientation of the drawing is indicated by the position of the substrate molecules HP and MgAMPCPP. (This figure was prepared with the program MOLSCRIPT [21].)

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1049-1058) copyright 2000.  
  Figure was selected by the author.  

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
18604568 C.Andreini, I.Bertini, G.Cavallaro, G.L.Holliday, and J.M.Thornton (2008).
Metal ions in biological catalysis: from enzyme databases to general principles.
  J Biol Inorg Chem, 13, 1205-1218.  
18323618 E.Nishibori, T.Nakamura, M.Arimoto, S.Aoyagi, H.Ago, M.Miyano, T.Ebisuzaki, and M.Sakata (2008).
Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data.
  Acta Crystallogr D Biol Crystallogr, 64, 237-247.  
17680687 M.Brylinski, and J.Skolnick (2008).
What is the relationship between the global structures of apo and holo proteins?
  Proteins, 70, 363-377.  
18652651 S.Santini, V.Monchois, N.Mouz, C.Sigoillot, T.Rousselle, J.M.Claverie, and C.Abergel (2008).
Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase.
  BMC Struct Biol, 8, 33.
PDB codes: 2g9z 2hh9
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
17039546 N.Nagano, T.Noguchi, and Y.Akiyama (2007).
Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
  Proteins, 66, 147-159.  
16365036 J.Y.Liu, D.E.Timm, and T.D.Hurley (2006).
Pyrithiamine as a substrate for thiamine pyrophosphokinase.
  J Biol Chem, 281, 6601-6607.
PDB code: 2f17
17132104 M.L.Eschbach, I.B.Müller, T.W.Gilberger, R.D.Walter, and C.Wrenger (2006).
The human malaria parasite Plasmodium falciparum expresses an atypical N-terminally extended pyrophosphokinase with specificity for thiamine.
  Biol Chem, 387, 1583-1591.  
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
14648615 N.Gresh, and G.B.Shi (2004).
Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation.
  J Comput Chem, 25, 160-168.  
14696187 S.Sarkhel, and G.R.Desiraju (2004).
N-H...O, O-H...O, and C-H...O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition.
  Proteins, 54, 247-259.  
14675548 B.W.Dijkstra, and R.G.Matthews (2003).
Catalysis and regulation - from structure to function.
  Curr Opin Struct Biol, 13, 706-708.  
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.  
12211000 O.Keskin, X.Ji, J.Blaszcyk, and D.G.Covell (2002).
Molecular motions and conformational changes of HPPK.
  Proteins, 49, 191-205.  
12039964 V.Illarionova, W.Eisenreich, M.Fischer, C.Haussmann, W.Romisch, G.Richter, and A.Bacher (2002).
Biosynthesis of tetrahydrofolate. Stereochemistry of dihydroneopterin aldolase.
  J Biol Chem, 277, 28841-28847.  
  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
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.