Isopeptide linkage

Goldknope, I. L. and Busch, H. Isopeptide linkage between nonhistone and histone 2A polypeptides of chromosomal conjugate-protein A24. Proc. Natl. Acad. USA, 1977, 74, 864-868. 

Figure 7 Multiple roles of the deubiquitinating enzymes. Deubiquitinating enzymes (DUBs) of the UCH type (dark scissors) process ubiquitin precursors. UCH-L1 generates monoubiquitins from tandemly linked ubiquitin gene product. UCH-L3 acts on ubiquitin synthesized as a protein fused to small ribosomal subunits. DUBs of the UBP type (shaded scissors) process ubiquitins linked in isopeptide linkage in polyubiquitin chains. DUBs also reverse the ubiquitination on erroneously targeted substrates (editing). Another important function of DUBs is disassembly of polyubiquitin chains as the ubiquitinated substrate is degraded. Ubiquitin attached to substrates after activation are indicated as lollipop-like structures with filled circles. Free ubiquitin or ubiquitin unit in precursor is shown with open circles.

The studies on specificity of UBPs with respect to isopeptide linkages of ubiquitin do not address the physiological substrate specificity, however. Although diverse substrates are polyubiquitinated, the nature of the isopeptide linkages of ubiquitin is the same in all substrates. Therefore, physiological specificity must arise from noncatalytic parts of the UBP molecules that interact with the substrates. A recent study shows that two... 

This enzyme [EC 3.4.19.5], now known as /3-aspartyl-peptidase, is a mammahan cytosolic protein that catalyzes the hydrolysis of a /3-hnked aspartyl residue from the N-terminus of a polypeptide. Other isopeptide linkages (e.g., a y-glutamyl hnkage) are not hydrolyzed by this enzyme. 

The third step of ubiquitinylation, the transfer of ubiquitin to the target protein, is catalyzed by a ubiquitin-protein-ligase, or E3 enzyme. In this reaction ubiquitin is linked by its C-terminal glycine in an amide isopeptide linkage to an e-NH2-group of the substrate proteins Lys residues. 

Another common crosslink is an amide formed between the y-carboxyl group of a glutamic acid side chain and an amino group from a lysine residue.307 This isopeptide linkage is formed from a residue of gluta-mine through the action of the enzyme transglutaminase (Eq. 2-23). Isopeptide crosslinks are found in hair, skin, connective tissue, and blood clots. 

Many short-lived proteins are degraded within the cytosol in ATP-dependent processes. A major process involves the small protein ubiquitin (Box 10-C).134 Once "labeled" by formation of an isopeptide linkage to ubiquitin, a peptide is attacked by proteases in the proteasome complexes (Box 7-A, Chapter 12). There it is quickly degraded. Other proteases, most of which do not require ATP, are also present in the cytoplasm (Chapter 12). How do these enzymes as well as those within the lysosomes work together to produce a harmonious turnover of the very substance of our tissues How is it possible that one protein has a long half life of many days while another lasts only an hour or two in the same cell The answer seems to be that... 

Isopentenyl diphosphate (prenyl pyrophosphate) 527, 689, 690s, 712s Isopentenyladenosine 234s Isopeptidases 525 Isopeptide linkage in proteins 80 to ubiquitin 524... 

Yang, Z., Pandi, L., and Doolitde, R. F. (2002). The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface. Biochem. 41, 15610-15617. 

Structure of folic acid showing its components. The numbered part participates in one-carbon transfer reactions. In nature, folate occurs largely as polyglutamyl derivatives in which the glutamate residues are attached by isopeptide linkages via the y-carboxyl group. The pteridine ring structure is also present in tetrahydrobiopterin, a coenzyme in the hydroxylation of phenylalanine, tyrosine, and tryptophan (Chapter 17). 

Synthesis of ubiquitinated peptides and proteins with the native isopeptide linkage is very challenging. During the development of chemical ubiquitination methods, researchers frequently need to balance the necessity for nativity of the ubiquitin linkage against the labor requirements of the synthetic task. Many relatively simple methods to generate non-native or mimetic ubiquitin conjugates have therefore been developed. 

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