Thioether protein crosslinks

From Proteopedia

Thioether bonds between the sidechains of cysteine and tyrosine have been well studied in cysteine dioxygenases^[1], and observed in catalase^[2] 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.

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.

Examples

Cys-Tyr

• 1gof (1991): Galactose oxidase.
• 1sy7 (2004): Catalase.
• 6e87 (2019): Cysteine dioxygenase.

Cys-Ligand

• 5nf0 (2017): Peptide cyclized via 2 thioethers with xylene.
• 6o83 (2019): Ubiquitin-activating enzyme E1 thioether-bonded to a modified deoxy adenosine.
• 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

In addition to the bonds discussed above, other covalent cross-links between polypeptide chains include:

• Disulfide bonds
• Isopeptide bonds
• Thioester protein crosslinks
• Ester protein crosslinks
• Histidine-tyrosine protein crosslinks
• Lysine-cysteine NOS bonds

References

1. ↑ Davies CG, Fellner M, Tchesnokov EP, Wilbanks SM, Jameson GN. The Cys-Tyr Crosslink of Cysteine Dioxygenase changes the Optimum pH of Reaction without Structural Change. Biochemistry. 2014 Nov 12. PMID:25390690 doi:http://dx.doi.org/10.1021/bi501277a
2. ↑ Diaz A, Horjales E, Rudino-Pinera E, Arreola R, Hansberg W. Unusual Cys-Tyr covalent bond in a large catalase. J Mol Biol. 2004 Sep 17;342(3):971-85. PMID:15342250 doi:10.1016/j.jmb.2004.07.027