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]. | ||
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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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In July, 2021, use of these records is inconsistent. Sometimes one is used, sometimes the other, sometimes some isopeptide bonds are in REMARK 500 CLOSE CONTACTS and other isopeptide bonds in the same model are in LINK records ([[5i6a]]), and sometimes isopeptide bonds that are present are not documented in either kind of record (e.g. [[1fma]] in July, 2021). In | In July, 2021, use of these records is inconsistent. Sometimes one is used, sometimes the other, sometimes some isopeptide bonds are in REMARK 500 CLOSE CONTACTS and other isopeptide bonds in the same model are in LINK records ([[5i6a]]), and sometimes isopeptide bonds that are present are not documented in either kind of record (e.g. [[1fma]] in July, 2021). In 2021, the [[wwPDB]] is considering remediation to properly annotate all isopeptide bonds<ref name="annotation">Remediation of the PDB database to guarantee proper annotation of all isopeptide bonds was discussed with Rachel Kramer Green of the RCSB in June, 2021.</ref>. See example PDB IDs below. | ||
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> | ||
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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, 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. | ||
==Examples== | ==Examples== | ||
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*[[5jqf]]: Lasso peptide sphingopyxin I has Asp9 isopeptide bonded to the amino terminus at Gly1. This bond is cleaved by lasso peptide isopeptidase. | *[[5jqf]]: Lasso peptide sphingopyxin I has Asp9 isopeptide bonded to the amino terminus at Gly1. This bond is cleaved by lasso peptide isopeptidase. | ||
== | ===Pyroglutamate=== | ||
[[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]] (PCA1) and [[2are]] (Gln1). Element color key: | ||
{{Template:ColorKey_Element_C}} | |||
{{Template:ColorKey_Element_O}} | |||
{{Template:ColorKey_Element_N}}. | |||
==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]]. | |||
==Other Types of Protein Crosslinks== | ==Other Types of Protein Crosslinks== | ||