Sandbox Reserved 717: Difference between revisions

'''The 33kDa Fragment''' <ref name=r3>PMID: 12888344</ref> <ref>PMID:11530935</ref>

The <scene name='Sandbox_Reserved_717/Myscene/11'>33kDa fragment</scene> (PDB:1H6W)  was generated in the presence of EDTA <ref name=r3>PMID: 12888344</ref>. This fragment contains the residues <scene name='Sandbox_Reserved_717/Myfirstscene/1'>85-395</scene> and <scene name='Sandbox_Reserved_717/Mysecondscene/1'>518-527</scene> .  The residues 397-517 are lacking because of internal deletion.

The 33kDa fragment can be further sub-divided into two subunits <ref name=r3>PMID: 12888344</ref>. The <scene name='Sandbox_Reserved_717/Mythirdscene/1'>neck</scene>  (residue 333-341) and the <scene name='Sandbox_Reserved_717/Myscene/12'>collar</scene> (residues <scene name='Sandbox_Reserved_717/Mythirdscene/2'>342-396 </scene> plus <scene name='Sandbox_Reserved_717/Mythirdscene/3'> 518-527</scene>). The neck connects the body of the fibre to its C-terminal collar and receptor-binding site. It consists of a triple alpha-helix which is built by the residues 333-341.

'''The 45kDa Fragment <ref name=r3>PMID: 12888344</ref>

For generating the 45kDa fragment the full length gp12 was co-expressed with its chaperone gp57 and purified <ref name=r3>PMID: 12888344</ref>. Like the 33kDa fragment it also starts with the amino acid Leu85. The 45kDa fragment contains the residues <scene name='Sandbox_Reserved_717/Mythirdscene/4'>397-517</scene> , which are in the 33kDa fragment internal deleted <ref name=r3>PMID: 12888344</ref> .

Like the 33kDa fragment the 45kDa fragment can also be divided into two subunits. These two subunits are called <scene name='Sandbox_Reserved_717/Myscene/13'>head </scene> (residues <scene name='Sandbox_Reserved_717/Mythirdscene/5'>397-446 </scene> and residues <scene name='Sandbox_Reserved_717/Mythirdscene/6'>487-517</scene> ) and <scene name='Sandbox_Reserved_717/Mythirdscene/7'>bonnet</scene>  (residues 447-487). On the border between the head and the bonnet subunit there is a metal-binding site <ref name=r3>PMID: 12888344</ref>.

'''Receptor-Binding Domain '''<ref name=r3>PMID: 12888344</ref>

Gp12 is fixed with its N-terminal domain to the baseplate. So the C-terminal domain has to be involved in LPS-binding. To detect where the receptor-binding domain is, full-length gp12, 33kDa fragments and 45kDa fragments were immobilised in micro-plate wells and were allowed to bind to bacteria <ref name=r3>PMID: 12888344</ref>. The result was that the 33kDa fragment did never bind to a bacteria <ref name=r3>PMID: 12888344</ref>. The 45kDa fragment did bind. So the receptor-binding domain is absent in the 33kDa fragment but present in the 45kDa fragment. The residues which are present in the 45kDa fragment and lacking in the 33kDa fragment are the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. They are referred to be part of the receptor-binding domain.

The receptor-binding domain can be sub-divided into head and bonnet. On the border between these two subdomains there is a metal-binding site <ref name=r3>PMID: 12888344</ref>. This site binds presumably to zinc. <scene name='Sandbox_Reserved_717/Mynewscene/3'>Two His amino acids </scene> (<scene name='Sandbox_Reserved_717/Mynewscene/1'>His445</scene> and <scene name='Sandbox_Reserved_717/Mynewscene/2'>His447</scene>) from each monomere are octahedrally coordinated around the zinc.  

'''The LPS-Bindind Site''' <ref name=r3>PMID: 12888344</ref>

The exact position of the lipo-polysaccharide(LPS)-binding site is not known. Proteolysis experiments showed, that it contains to the domain with the residues <scene name='Sandbox_Reserved_717/Mythirdscene/8'>397-517</scene>. Compared with the homologous bacteriophage T4-like strain AR1 sequence, which also binds to the same LPS core molecule like gp12, there can be some possible binding residues be assumed.