Thioester protein crosslinks: Difference between revisions

Latest revision as of 20:50, 9 November 2023

Thioester bonds between cysteine and glutamine sidechains can form covalent cross-links between polypeptide chains. An accurate estimate of the number of thioester bonds in the PDB may not be available (see Protein crosslinks#Thioester Crosslinks). A search for "thioester" in Proteopedia yields >500 hits.

Thioester bonds are one way that ubiquitin may be attached to proteins (ubiquitinylation; see also Ubiquitin and Ubiquitination).

Thioester bonds in complement proteins C3 and C4 are involved in tagging pathogens for destruction by the immune system, via the alternate complement activation pathway. Example: 2b39.

Thioester bonds occur in thioester domains (TED) of Gram-positive bacteria, where they are thought to mediate covalent adhesion of bacteria to host cells^[1]^[2], or to participate in bacterial conjugation involved in antibiotic resistance^[3]. Many surface proteins of Gram-positive bacteria are predicted to contain TED as well as isopeptide and ester cross-links. This family of proteins is termed TIE proteins for thioester, isopeptide, ester proteins^[2]. Examples: 2xi9, 6fwy.
- In a dramatic example, the pilus tip adhesin of Streptococcus pyogenes forms dimers in the presence of spermidine, a di-amine that forms thiopeptide bonds with the Gln211 residues in two adhesin protein chains, illustrated in 4c0z^[4].

Detection and VisualizationDetection 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 CrosslinksOther Protein Crosslinks

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

ReferencesReferences

↑ Nakata M, Kreikemeyer B. Genetics, Structure, and Function of Group A Streptococcal Pili. Front Microbiol. 2021 Feb 9;12:616508. doi: 10.3389/fmicb.2021.616508., eCollection 2021. PMID:33633705 doi:http://dx.doi.org/10.3389/fmicb.2021.616508
↑ ^2.0 ^2.1 Miller OK, Banfield MJ, Schwarz-Linek U. A new structural class of bacterial thioester domains reveals a slipknot topology. Protein Sci. 2018 Jul 27. doi: 10.1002/pro.3478. PMID:30052296 doi:http://dx.doi.org/10.1002/pro.3478
↑ Gago-Cordoba C, Val-Calvo J, Abia D, Diaz-Talavera A, Miguel-Arribas A, Aguilar Suarez R, van Dijl JM, Wu LJ, Meijer WJJ. A Conserved Class II Type Thioester Domain-Containing Adhesin Is Required for Efficient Conjugation in Bacillus subtilis. mBio. 2021 Mar 16;12(2). pii: mBio.00104-21. doi: 10.1128/mBio.00104-21. PMID:33727345 doi:http://dx.doi.org/10.1128/mBio.00104-21
↑ Linke-Winnebeck C, Paterson NG, Young PG, Middleditch MJ, Greenwood DR, Witte G, Baker EN. Structural model for the covalent adhesion of the Streptococcus pyogenes pilus through a thioester bond. J Biol Chem. 2013 Nov 12. PMID:24220033 doi:http://dx.doi.org/10.1074/jbc.M113.523761

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

[nakata2021-1] Nakata M, Kreikemeyer B. Genetics, Structure, and Function of Group A Streptococcal Pili. Front Microbiol. 2021 Feb 9;12:616508. doi: 10.3389/fmicb.2021.616508., eCollection 2021. PMID:33633705 doi:http://dx.doi.org/10.3389/fmicb.2021.616508

[slipknot-2] 2.0 ^2.1 Miller OK, Banfield MJ, Schwarz-Linek U. A new structural class of bacterial thioester domains reveals a slipknot topology. Protein Sci. 2018 Jul 27. doi: 10.1002/pro.3478. PMID:30052296 doi:http://dx.doi.org/10.1002/pro.3478

[gago-cordoba-3] Gago-Cordoba C, Val-Calvo J, Abia D, Diaz-Talavera A, Miguel-Arribas A, Aguilar Suarez R, van Dijl JM, Wu LJ, Meijer WJJ. A Conserved Class II Type Thioester Domain-Containing Adhesin Is Required for Efficient Conjugation in Bacillus subtilis. mBio. 2021 Mar 16;12(2). pii: mBio.00104-21. doi: 10.1128/mBio.00104-21. PMID:33727345 doi:http://dx.doi.org/10.1128/mBio.00104-21

[linke-winnebeck2014-4] Linke-Winnebeck C, Paterson NG, Young PG, Middleditch MJ, Greenwood DR, Witte G, Baker EN. Structural model for the covalent adhesion of the Streptococcus pyogenes pilus through a thioester bond. J Biol Chem. 2013 Nov 12. PMID:24220033 doi:http://dx.doi.org/10.1074/jbc.M113.523761

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 ==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 under ''Examples'' to go to a Proteopedia page titled with a 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]].
+[[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==