Thioether protein crosslinks: Difference between revisions
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Thioether bonds between the sidechains of '''cysteine and tyrosine''' have been well studied in cysteine dioxygenases<ref>PMID:25390690</ref>, and observed in catalase and galactose oxidase (see examples below). | Thioether bonds between the sidechains of '''cysteine and tyrosine''' have been well studied in cysteine dioxygenases<ref>PMID:25390690</ref>, and observed in catalase<ref name="diaz2004">PMID: 15342250</ref> and galactose oxidase (see examples below). | ||
Thioether bonds between cysteine and ligands are common, but are generally not crosslinks between polypeptides. Thioether bonds between '''cysteine and the vinyl groups of hemes''' are common. Diverse other '''ligands''' are bonded to protein via cysteine thioether linkages. | Thioether bonds between cysteine and ligands are common, but are generally not crosslinks between polypeptides. Thioether bonds between '''cysteine and the vinyl groups of hemes''' are common. Diverse other '''ligands''' are bonded to protein via cysteine thioether linkages. | ||
Note that the sidechain of methionine contains a thioether. | Note that the '''sidechain of methionine''' contains a thioether (which is not a protein crosslink). | ||
An accurate estimate of the frequency of thioether crosslinks in the [[PDB]] may not be available. A search for "thioether" in Proteopedia yields >200 hits in abstracts of pages titled with 4-character [[PDB codes]]. | An accurate estimate of the frequency of thioether crosslinks in the [[PDB]] may not be available. A search for "thioether" in Proteopedia yields >200 hits in abstracts of pages titled with 4-character [[PDB codes]]. | ||
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* [[6o83]] (2019): Ubiquitin-activating enzyme E1 thioether-bonded to a modified deoxy adenosine. | * [[6o83]] (2019): Ubiquitin-activating enzyme E1 thioether-bonded to a modified deoxy adenosine. | ||
* [[6vdq]] (2021): Bacterial peroxygenase thioether-bonded to heme. | * [[6vdq]] (2021): Bacterial peroxygenase thioether-bonded to heme. | ||
==Detection and Visualization== | |||
[[FirstGlance in Jmol]] alerts you to protein crosslinks when present, and provides convenient links that zoom in and and display each one in detail. Viewing the [[electron density map]] is just one more click. Use the links above to 4-character [[PDB codes]] to go to a Proteopedia page titled with that 4-character [[PDB code]]. There, click on "FirstGlance". In FirstGlance, click on the Tools tab, and there, on "Protein Crosslinks". See the practical guide [[FirstGlance/Evaluating Protein Crosslinks]]. | |||
==Other Protein Crosslinks== | ==Other Protein Crosslinks== | ||
In addition to the | In addition to the bonds discussed above, other [[Protein crosslinks|covalent cross-links between polypeptide chains]] include: | ||
*[[Disulfide bond]]s | *[[Disulfide bond]]s | ||
*[[Isopeptide bond]]s | *[[Isopeptide bond]]s | ||
*[[Thioester protein crosslinks]] | *[[Thioester protein crosslinks]] | ||
*[[Ester protein crosslinks]] | *[[Ester protein crosslinks]] | ||
*[[Histidine-tyrosine protein crosslinks]] | |||
*[[Lysine-cysteine NOS bonds]] | *[[Lysine-cysteine NOS bonds]] | ||
==References== | ==References== | ||
<references /> | <references /> | ||