Isopeptide bond: Difference between revisions
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For more, please see [http://en.wikipedia.org/wiki/Isopeptide_bond Isopeptide bond in Wikipedia]. | For more, please see [http://en.wikipedia.org/wiki/Isopeptide_bond Isopeptide bond in Wikipedia]. | ||
==Functions== | |||
In addition to the cases listed here, see more functions below under [[#Examples|Examples]]. | |||
* The isopeptide bond in [[9y31]] is believed to facilitate expulsion of RNA into the host cell by a non-enveloped icosahedral plant virus, [[9y2z]].<ref>PMID: 41385643</ref> | |||
==Formation== | ==Formation== | ||
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*Intermolecular (between molecule) "chain mail" isopeptide bonds in the capsid of bacteriophage HK97<ref name="wikoff2000" />. | *Intermolecular (between molecule) "chain mail" isopeptide bonds in the capsid of bacteriophage HK97<ref name="wikoff2000" />. | ||
*Engineered intramolecular isopeptide bonds between collagen mimetic peptides<ref>PMID: 32820897</ref>. | *Engineered intramolecular isopeptide bonds between collagen mimetic peptides<ref>PMID: 32820897</ref>. | ||
===Autocatalytic=== | |||
''De novo'' design of proteins capable of autocatalytic isopeptide bond formation was reported in 2025<ref>PMID: 40138671</ref>. Structures are [[9mxw]] and [[9mxx]]. | |||
===Enzymatic=== | ===Enzymatic=== | ||
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Here are the relevant LINK records from [[3htl]]:<pre> | Here are the relevant LINK records from [[3htl]]:<pre> | ||
LINK NZ LYS X 199 CG ASN X 321 1555 1555 1.43 | LINK NZ LYS X 199 CG ASN X 321 1555 1555 1.43 | ||
LINK NZ LYS X 363 CG ASN X 482 1555 1555 1.55</pre> | LINK NZ LYS X 363 CG ASN X 482 1555 1555 1.55</pre> | ||
Note that link records involving MSE ([[selenomethionine]]) generally signify nothing more than MSE being part of a polypeptide chain, but are required because the [[Hetero atoms|HETATM]] MSE residue is covalently linked to the adjacent standard amino acids. Similarly, all covalent connections to D-amino acids [[5i6a]] and ligands should be listed in LINK records. | Note that link records involving MSE ([[selenomethionine]]) generally signify nothing more than MSE being part of a polypeptide chain, but are required because the [[Hetero atoms|HETATM]] MSE residue is covalently linked to the adjacent standard amino acids. Similarly, all covalent connections to D-amino acids [[5i6a]] and ligands should be listed in LINK records. | ||
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==Detection and Visualization== | ==Detection and Visualization== | ||
[[FirstGlance in Jmol]] alerts you to isopeptide bonds when present, and provides convenient links to that zoom 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 isopeptide bonds when present, and provides convenient links to that zoom 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]] and the [[Image:Youtube.png]] [https://www.youtube.com/watch?v=fjir4cqsI3U video demonstration]. | ||
==Other Types of Protein Crosslinks== | ==Other Types of Protein Crosslinks== | ||
