Isopeptide bond: Difference between revisions
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<Structure load='' size='350' frame='true' align='right' caption='' scene='56/560856/Isopeptide_bond/4' /> | <Structure load='' size='350' frame='true' align='right' caption='' scene='56/560856/Isopeptide_bond/4' /> | ||
An ''isopeptide bond'' is an [ | An ''isopeptide bond'' is an [http://en.wikipedia.org/wiki/Amide amide bond] between the sidechain of one [[amino acid]] and the sidechain or main chain terminus of another amino acid, or a ligand. Isopeptide bonds are sometimes called [http://en.wikipedia.org/wiki/Lactam lactams]<ref name="lactam">PMID: 24446383</ref><ref name="5vbl">PMID: 28528775</ref>.<br>[[Image:Isopeptide-bond.jpg|300px]] | ||
Isopeptide bonds | Isopeptide bonds can form covalent links between polypeptide backbones. This is in contrast to the much more common [[Peptide bond|peptide (''eupeptide'') bonds]] between amino acid main chain atoms that form the polypeptide backbones of proteins. Isopepide bonds are rare (as are other non-disulfide [[protein crosslinks]]). [[Disulfide bonds]] are a much more common form of covalent linkage between polypeptide chains. | ||
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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==Frequency== | ==Frequency== | ||
A search for ''isopeptide bond'' in the keywords records at the [[PDB]] returns about 200 hits (April, 2021). This suggests that approximately one model per thousand in the [[PDB]] contains isopeptide bonds. However, not all entries containing the term ''isopeptide'' actually have isopeptide bonds in the [[asymmetric unit]], and some entries that do have isopeptide bonds do not | A search for ''isopeptide bond'' in the keywords records at the [[PDB]] returns about 200 hits (April, 2021). This suggests that approximately one model per thousand in the [[PDB]] contains isopeptide bonds. However, not all entries containing the term ''isopeptide'' actually have isopeptide bonds in the [[asymmetric unit]], and some entries that do have isopeptide bonds do not contain the word "isopeptide" anywhere in their PDB files. | ||
==PDB KEYWDS, REMARK 500, and LINK Records== | ==PDB KEYWDS, REMARK 500, and LINK Records== | ||
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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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===Pyroglutamate=== | ===Pyroglutamate=== | ||
[[Image:2are-gln1-chain-A.png|right| | [[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 bond. See [ | 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_O}} | |||
{{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". 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== | ||
