What does mean HHHHHH in structures? histidine? can i replace X signs with H when I predict secondary structure of protein pdb? (Im testing my program)
its amino acid seqence,,,, example
Looks like real sequence of a viral intrgrase
>pdb|2M9U|A Chain A, Integrase p46
Query 1 HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAAD 60
Sbjct 1 HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAAD 60
Query 61 PGGGPSSRLTWRVQRSQNPLKIRLTREAP 89
Sbjct 61 PGGGPSSRLTWRVQRSQNPLKIRLTREAP 89
because its real xD
It is a His6 tag which is used for metal-chelating column purification. At neutral or slightly basic pH, consecutive histidines chelate metals which are immobilized on a solid column surface.
These tags can be found at either protein's end, but more frequently at the C-terminus. They are usually not resolved in crystal structures because of floppiness.
They are also not usually present in crystal structures because usually they are cleaved off if used as part of an IMAC process since they can impair crystal formation. Typically you would have something like HHHHHH-CS-Protein, where the CS is a thrombin cleavage site or similar.
Some people cleave His-tags off, others don't. It is a matter of personal experience and preference, because many proteins have been crystallized with His-tags. A quick grep for HHHHHH against protein sequences extracted from PDB shows more than 83 thousand lines with the His6 pattern, and that's probably a lower-bound estimate.
A simple rule of thumb: whenever the His-tag is included in the SEQRES record of PDB files, it means that the tag itself was part of the protein that was subjected to crystallization or NMR spectroscopy. I have not seen more than 2 of those 6 histidines actually modeled in crystal structures, and most often none of them are for reasons of conformational flexibility.
thank you :)
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