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PDBsum entry 1tmj

Go to PDB code: 
protein metals links
Transferase PDB id
1tmj
Jmol PyMol
Contents
Protein chain
158 a.a. *
Metals
_CL
_MG ×2
Waters ×252
* Residue conservation analysis
PDB id:
1tmj
Name: Transferase
Title: Crystal structure of e.Coli apo-hppk(w89a) at 1.45 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. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: folk, b0142. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.45Å     R-factor:   0.155     R-free:   0.174
Authors: J.Blaszczyk,X.Ji
Key ref:
Y.Li et al. (2005). Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies. Biochemistry, 44, 8590-8599. PubMed id: 15952765 DOI: 10.1021/bi0503495
Date:
10-Jun-04     Release date:   21-Jun-05    
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
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8- dihydropterin diphosphate
ATP
+ 6-hydroxymethyl-7,8-dihydropterin
= AMP
+ 6-hydroxymethyl-7,8- dihydropterin diphosphate
      Cofactor: Mg(2+)
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  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi0503495 Biochemistry 44:8590-8599 (2005)
PubMed id: 15952765  
 
 
Is the critical role of loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase in catalysis due to loop-3 residues arginine-84 and tryptophan-89? Site-directed mutagenesis, biochemical, and crystallographic studies.
Y.Li, J.Blaszczyk, Y.Wu, G.Shi, X.Ji, H.Yan.
 
  ABSTRACT  
 
Deletion mutagenesis, biochemical, and X-ray crystallographic studies have shown that loop 3 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is required for the assembly of the active center, plays an important role in the stabilization of the ternary complex of HPPK with MgATP and 6-hydroxymethyl-7,8-dihydropterin (HP), and is essential for catalysis. Whether the critical functional importance of loop 3 is due to the interactions between residues R84 and W89 and the two substrates has been addressed by site-directed mutagenesis, biochemical, and X-ray crystallographic studies. Substitution of R84 with alanine causes little changes in the dissociation constants and kinetic constants of the HPPK-catalyzed reaction, indicating that R84 is not important for either substrate binding or catalysis. Substitution of W89 with alanine increases the K(d) for the binding of MgATP by a factor of 3, whereas the K(d) for HP increases by a factor of 6, which is due to the increase in the dissociation rate constant. The W89A mutation decreases the rate constant for the chemical step of the forward reaction by a factor of 15 and the rate constant for the chemical step of the reverse reaction by a factor of 25. The biochemical results of the W89A mutation indicate that W89 contributes somewhat to the binding of HP and more significantly to the chemical step. The crystal structures of W89A show that W89A has different conformations in loops 2 and 3, but the critical catalytic residues are positioned for catalysis. When these results are taken together, they suggest that the critical functional importance of loop 3 is not due to the interactions of the R84 guanidinium group or the W89 indole ring with the substrates.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.

 

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