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 is an example of the relevant REMARK 500 records from [[2xi9]]. The lines with ATM1=NZ are isopeptide bonds; those with ATM1=SG are [[Thioester protein crosslinks|thioester bonds]].<pre> | Here is an example of the relevant REMARK 500 records from [[2xi9]]. The lines with ATM1=NZ are isopeptide bonds; those with ATM1=SG are [[Thioester protein crosslinks|thioester bonds]].<pre> | ||
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. | REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. | ||
REMARK 500 | |||
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE | REMARK 500 | ||
REMARK 500 NZ LYS B 297 CG ASP B 595 1.31 | |||
REMARK 500 NZ LYS A 297 CG ASP A 595 1.32 | REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE | ||
REMARK 500 SG CYS B 426 CD GLN B 575 1.63 | |||
REMARK 500 NZ LYS B 297 CG ASP B 595 1.31 | |||
REMARK 500 NZ LYS A 297 CG ASP A 595 1.32 | |||
REMARK 500 SG CYS B 426 CD GLN B 575 1.63 | |||
REMARK 500 SG CYS A 426 CD GLN A 575 1.64</pre> | REMARK 500 SG CYS A 426 CD GLN A 575 1.64</pre> | ||
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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[[Image:2are-gln1-chain-A-225px.png|right|frame|Pyroglutamate with electron density map]] | [[Image:2are-gln1-chain-A-225px.png|right|frame|Pyroglutamate with electron density map]] | ||
N-terminal Glu or Gln can cyclize, forming an internal lactam (isopeptide) bond. See [http://en.wikipedia.org/wiki/Pyroglutamic_acid Pyroglutamic acid in Wikipedia]. Examples with convincing electron densities include [[1s1a]] and [[2are]]. Element color key: | N-terminal Glu or Gln can cyclize, forming an internal lactam (isopeptide) bond. See [http://en.wikipedia.org/wiki/Pyroglutamic_acid Pyroglutamic acid in Wikipedia]. Examples with convincing electron densities include [[1s1a]] (PCA1) and [[2are]] (Gln1). Element color key: | ||
{{Template:ColorKey_Element_C}} | {{Template:ColorKey_Element_C}} | ||
{{Template:ColorKey_Element_O}} | {{Template:ColorKey_Element_O}} | ||
{{Template:ColorKey_Element_N}}. | {{Template:ColorKey_Element_N}}. | ||
==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". | [[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== | ||
