XLH Research

Mutation to the PHEX protein is responsible for XLH. Although the primary sequence of the protein is known for years, no cristallographic 3-D model is available so far. 

 

By running sequence alignment tools, the best match of amino acid sequence is found between PHEX and NEP (neprilysin, another protein belonging, as PHEX, to the M13 family of endoproteinase). Fortunately, the cristallographic model of NEP is available.

 

By molecular threading, it is possible to use the NEP model as a template and to build a 3-D model of PHEX. You will find below the first picture of the PHEX model. This is a preliminary result and it will be refined to take into account as much as possible of the topological constraints resulting from the divergent amino acid regions of PHEX.

 

 

Colors are set by secondary structure types : helix in yellow, beta strand in red, coil/random in white.  

 

To assess the quality of this first-wave model, let's compare the topology of a highly conserved feature of the M13 endopeptidase: the Zinc-binding motif. Entrapping of the zinc ion is realized by a kind of electrostatic trap made of 3 residues: 2 Histidines and 1 Glutamic acid. Below, these 3 residues have been isolated from both the experimental model of NEP (left) and the homology model of PHEX (right). Distances measured between atoms are presented in yellow (in Å).

 

 

 

Obviously, the PHEX homology model is not able to reproduce accurately the perfect triangular shape of the Zn binding motif of NEP. Back to the bench...

 

Enhancement of the homology model of PHEX.

 

By introducing a gap just before Leu532, the overall downstream sequence alignment is enhanced, showing optimal aligment in the 500 to 700 res. region. Morevoer, the conformation of the Zn-binding motif is very well correlated to that of the NEP model (see below).

 

 

This leads to the following optimized model:

 

 

While a different display has been used to generate this view, the overall shape of the molecule is very similar to the previous picture (see top of this page). Note the 'hole' in the center of the protein.