What does mean HHHHHH in structures?
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7 months ago
Xylanaser ▴ 80

Hey 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)

structure protein pdb • 393 views
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helix ?

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its amino acid seqence,,,, example

>001124152|e2m9uA1|4.1.1.114|A:1-89
HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAADPGGGPSSRLTWRVQRSQNPLKIRLTREAP
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Looks like real sequence of a viral intrgrase

>pdb|2M9U|A Chain A, Integrase p46
HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAADPGGGPSSRLT
WRVQRSQNPLKIRLTREAP

Query  1   HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAAD  60
           HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAAD
Sbjct  1   HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAAD  60

Query  61  PGGGPSSRLTWRVQRSQNPLKIRLTREAP  89
           PGGGPSSRLTWRVQRSQNPLKIRLTREAP
Sbjct  61  PGGGPSSRLTWRVQRSQNPLKIRLTREAP  89
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because its real xD

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7 months ago
Mensur Dlakic ★ 14k

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.

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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.

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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.

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thank you :) all best

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