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PDBsum entry 1ru1

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protein ligands metals links
Transferase PDB id
1ru1
Jmol
Contents
Protein chains
143 a.a. *
152 a.a. *
Ligands
APC ×2
PH2 ×2
Metals
_MG ×4
_CL
Waters ×481
* Residue conservation analysis
PDB id:
1ru1
Name: Transferase
Title: Crystal structure of a ternary complex of e. Coli hppk(v83g/del84-89) with mgampcpp and 6-hydroxymethyl-7,8- dihydropterin at 1.40 angstrom resolution (monoclinic form)
Structure: 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase. Chain: a, b. Synonym: 7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase, hppk, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, pppk. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: folk, b0142. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.40Å     R-factor:   0.150     R-free:   0.198
Authors: J.Blaszczyk,X.Ji
Key ref:
J.Blaszczyk et al. (2004). Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry, 43, 1469-1477. PubMed id: 14769023 DOI: 10.1021/bi036053l
Date:
10-Dec-03     Release date:   24-Feb-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.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P26281  (HPPK_ECOLI) -  2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Seq:
Struc:
159 a.a.
152 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: 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: 10.1021/bi036053l Biochemistry 43:1469-1477 (2004)
PubMed id: 14769023  
 
 
Essential roles of a dynamic loop in the catalysis of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
J.Blaszczyk, Y.Li, Y.Wu, G.Shi, X.Ji, H.Yan.
 
  ABSTRACT  
 
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the transfer of pyrophosphoryl group from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP) following an ordered bi-bi mechanism with ATP as the first substrate. The rate-limiting step of the reaction is product release, and the complete active center is assembled and sealed only upon the binding of both ATP and HP. The assembly of the active center involves large conformational changes in three catalytic loops, among which loop 3 undergoes the most dramatic and unusual changes. To investigate the roles of loop 3 in catalysis, we have made a deletion mutant, which has been investigated by biochemical and X-ray crystallographic analysis. The biochemical data showed that the deletion mutation does not have significant effects on the dissociation constants or the rate constants for the binding of the first substrate MgATP or its analogues. The dissociation constant of HP for the mutant increases by a factor of approximately 100, which is due to a large increase in the dissociation rate constant. The deletion mutation causes a shift of the rate-limiting step in the reaction and a decrease in the rate constant for the chemical step by a factor of approximately 1.1 x 10(5). The crystal structures revealed that the deletion mutation does not affect protein folding, but the catalytic center of the mutant is not fully assembled even upon the formation of the ternary complex and is not properly sealed. The results together suggest that loop 3 is dispensable for the folding of the protein and the binding of the first substrate MgATP, but is required for the assembling and sealing of the active center. The loop plays an important role in the stabilization of the ternary complex and is critical for catalysis.
 

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
19184528 R.Janowski, S.Panjikar, A.N.Eddine, S.H.Kaufmann, and M.S.Weiss (2009).
Structural analysis reveals DNA binding properties of Rv2827c, a hypothetical protein from Mycobacterium tuberculosis.
  J Struct Funct Genomics, 10, 137-150.
PDB code: 1zel
17680687 M.Brylinski, and J.Skolnick (2008).
What is the relationship between the global structures of apo and holo proteins?
  Proteins, 70, 363-377.  
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
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.  
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.