Isopeptide bond
From Proteopedia
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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 | + | 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ 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
