Question

What does mean HHHHHH in structures?

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3.1 years 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 • 1.3k views

ADD COMMENT • link updated 3.1 years ago by Mensur Dlakic ★ 27k • written 3.1 years ago by Xylanaser ▴ 80

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helix ?

ADD REPLY • link 3.1 years ago by Pierre Lindenbaum 161k

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its amino acid seqence,,,, example

>001124152|e2m9uA1|4.1.1.114|A:1-89
HHHHHHSHMVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAADPGGGPSSRLTWRVQRSQNPLKIRLTREAP

ADD REPLY • link updated 3.1 years ago by GenoMax 142k • written 3.1 years ago by Xylanaser ▴ 80

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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

ADD REPLY • link 3.1 years ago by GenoMax 142k

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because its real xD

ADD REPLY • link 3.1 years ago by Xylanaser ▴ 80

score 4 · Accepted Answer · 2021-03-16

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3.1 years ago

Mensur Dlakic ★ 27k

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.

ADD COMMENT • link 3.1 years ago by Mensur Dlakic ★ 27k

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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.

ADD REPLY • link 3.1 years ago by Joe 21k

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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.