This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


Isopeptide bond

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 7: Line 7:
The capsid of the HK97 bacteriophage contains isopeptide bonds that cross-link the protein [[chains]] into a protein ''chain mail'' <ref>PMID: 22297521</ref><ref>PMID: 10572124</ref><ref>PMID: 19091865</ref>.
The capsid of the HK97 bacteriophage contains isopeptide bonds that cross-link the protein [[chains]] into a protein ''chain mail'' <ref>PMID: 22297521</ref><ref>PMID: 10572124</ref><ref>PMID: 19091865</ref>.
-
Structures containing isopeptide bonds usually have "ISOPEPTIDE BOND" in their PDB file KEYWDS record, and should always have a LINK record indicating the isopeptide-bonded residues. Here are the relevant LINK records from [[3htl]]:<pre>
+
Structures containing isopeptide bonds usually have "ISOPEPTIDE BOND" in their PDB file KEYWDS record, and should always have LINK records indicating the isopeptide-bonded residues. 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 generally signify nothing more than MSE being part of a polypeptide chain, but are required because the HETATM MSE residue is covalently linked to the adjacent standard amino acids.
Examples:
Examples:

Revision as of 21:54, 26 April 2021


See Isopeptide bond in Wikipedia.

A search for isopeptide bond in the keywords records at the PDB returns over 200 hits (April, 2021).

The capsid of the HK97 bacteriophage contains isopeptide bonds that cross-link the protein chains into a protein chain mail [1][2][3].

Structures containing isopeptide bonds usually have "ISOPEPTIDE BOND" in their PDB file KEYWDS record, and should always have LINK records indicating the isopeptide-bonded residues. Here are the relevant LINK records from 3htl:
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

Note that link records involving MSE generally signify nothing more than MSE being part of a polypeptide chain, but are required because the HETATM MSE residue is covalently linked to the adjacent standard amino acids.

Examples:

  • 7cap is a ubiquitin homotrimer. The C-terminal Gly76 is isopeptide linked to Lys48 in each inter-chain interface[4].
  • 4mli contains the SpyTag peptide (which can be linked to a protein of interest) forming an isopeptide bond between SpyTag peptide Lys31 and SpyCatcher protein Asp117[5].
  • 3htl is a pilus monomer with isopepide bond Lys199-Asn321 and Lys363-Asn482.

References

  1. ↑ Hendrix RW, Johnson JE. Bacteriophage HK97 capsid assembly and maturation. Adv Exp Med Biol. 2012;726:351-63. doi: 10.1007/978-1-4614-0980-9_15. PMID:22297521 doi:10.1007/978-1-4614-0980-9_15
  2. ↑ Gilakjan ZA, Kropinski AM. Cloning and analysis of the capsid morphogenesis genes of Pseudomonas aeruginosa bacteriophage D3: another example of protein chain mail? J Bacteriol. 1999 Dec;181(23):7221-7. PMID:10572124
  3. ↑ Dierkes LE, Peebles CL, Firek BA, Hendrix RW, Duda RL. Mutational analysis of a conserved glutamic acid required for self-catalyzed cross-linking of bacteriophage HK97 capsids. J Virol. 2009 Mar;83(5):2088-98. doi: 10.1128/JVI.02000-08. Epub 2008 Dec 17. PMID:19091865 doi:10.1128/JVI.02000-08
  4. ↑ Hiranyakorn M, Yanaka S, Satoh T, Wilasri T, Jityuti B, Yagi-Utsumi M, Kato K. NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains. Int J Mol Sci. 2020 Jul 28;21(15). pii: ijms21155351. doi: 10.3390/ijms21155351. PMID:32731397 doi:http://dx.doi.org/10.3390/ijms21155351
  5. ↑ Li L, Fierer JO, Rapoport TA, Howarth M. Structural Analysis and Optimization of the Covalent Association between SpyCatcher and a Peptide Tag. J Mol Biol. 2013 Oct 23. pii: S0022-2836(13)00666-9. doi:, 10.1016/j.jmb.2013.10.021. PMID:24161952 doi:http://dx.doi.org/10.1016/j.jmb.2013.10.021

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Joel L. Sussman

Retrieved from "http://52.214.119.220/wiki/index.php/Isopeptide_bond"
Personal tools