Proteins isopeptides

Butler, M.R, Hanly, J. A., Moynagh, RN. Kinase-active interleukin-1 receptor-associated kinases promote polyubiquitination and degradation of the Pellino family direct evidence for PELLINO proteins being ubiquitin-protein isopeptide ligases. 1 Biol Chem 282 (2007) 29729-29737. 

Bhandari, D., Trejo, J., Benovic, J. L., Marchese, A. (2007). Arrestin-2 interacts vrnth the ubiquitin-protein isopeptide ligase atrophin-interacting protein 4 and mediates endosomal sorting of the chemokine receptor CXCR4. Journal of Biological Chemistry, 282, 36971-36979. 

Small tfbiquitin-like modifier represents a family of evolutionary conserved proteins that are distantly related in amino-acid sequence to ubiquitin, but share the same structural folding with ubiquitin proteins. SUMO proteins are covalently conjugated to protein substrates by an isopeptide bond through their carboxyl termini. SUMO addition to lysine residues of target proteins, termed SUMOylation, mediates post-transla-tional modification and requires a set of enzymes that are distinct from those that act on ubiquitin. SUMOylation regulates the activity of a variety of tar get proteins including transcription factors. 

Small Ubiquitin-like modifier (SUMO) is a conserved protein that is ubiquitously expressed in eukaryotes and is essential for viability. It serves as a reversible posttranslational modifier by forming an isopeptide bond with lysine residues in many target proteins, in a catalytic process termed SUMOylation. SUMOylation of proteins results in altered inter- or intramolecular interactions of the modified target (Fig. 1). 

The transglutaminases are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the /-carboxyl group of a glutamine in one polypeptide chain and the e-amino group of a lysine in the second (Greenberg et al., 1991). These... 

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.

Heating of foods rich in proteins may lead to formation of crosslinking isopeptide bonds between the S-NH2 group of lysine and the p- and y-carboxyl groups of aspartic and glutamic acid residues or their amides. 

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. 

These enzymes [EC 6.3.2.19] catalyze the reaction of ATP with ubiquitin and a lysyl residue in a protein to produce a protein containing an iV-ubiquityllysyl residue, AMP, and pyrophosphate (or, diphosphate). Ubiquitin is coupled to the protein by an isopeptide bond between the C-terminal glycine of ubiquitin and -amino groups of lysyl residues in the protein. An intermediate in the reaction contains one ubiquitin residue bound as a thi-olester to the enzyme, and a residue of ubiquitin adenylate noncovalently bound to the enzyme. 

The isopeptide bond between Ub and other proteins can be hydrolyzed there are multiple, ATP-independent proteases (the yeast Saccharomyces cerevisiae has at least 20 of them) whose common property is the ability to recognize Ub moiety and cleave at the Ub-adduct junction. One cause of the striking multiplicity of these deubiquitylating enzymes (DUBs) (17) is the diversity of their targets, which include linear (DNA-encoded) Ub fusions, Ub adducts with small nucleophiles such as glutathione, and also free and substrate-linked multi-Ub chains. 

Fig. 1. A schematic diagram outlining the hierarchic structure of the ubiquitin system. In an ATP-dependent manner a thioester bond is formed between the C-terminus of ubiquitin and an internal cystein residue of the ubiquitin-activating enzyme. Subsequently, ubiquitin is transferred to a member of the family of ubiquitin-conjugating enzymes, which are also able to form a thioester bond with ubiquitin. The third class of enzymes, the ubiquitin ligases, direct ubiquitin to the proteolytic substrates. Different families of this class of enzymes are known, some of which are also able to form a thioester intermediate with ubiquitin (HECT-domain ligases). The final ubiquitin-substrate linkage is an isopeptide bond between the C-terminus of ubiquitin and internal lysine residues in the substrate proteins...

A peptide is any compound produced by amide formation between a carboxyl group of one amino acid and an amino group of another. The amide bonds in peptides are called peptide bonds. The word peptide is usually applied to compounds whose amide bonds (sometimes called eupeptide bonds) are formed between C-1 of one amino acid and N-2 of another, but it includes compounds with residues linked by other amide bonds (sometimes called isopeptide bonds). Peptides with fewer than about 10-20 residues may also be called oligopeptides those with more residues are called polypeptides. Polypeptides of specific sequence of more than about 50 residues are usually known as proteins, but authors differ greatly on where they start to apply this term. 

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. 

It now appears more likely that gut enzymes may be responsible for partial isopeptide hydrolysis (22). Waibel and Carpenter (11) suggest that hydrolysis may occur within the intestinal wall after absorption of the isopeptide. However, these studies on absorption of the free e(Y-L-glutamyl)-L-lysine may not be relevant to cross-links in an overheated protein. 

It may be concluded that cross-linking due to isopeptide formation is probably responsible for decreased overall digestibility of the protein (, 22) thus, if the digestive enzymes are not able to release the smaller peptides, then the question of availability of the isopeptides per se is beside the point. Ford (13) points out that the rate of digestibility of isopeptide links may preclude the maximum availability of the lysine as a result of the lysine entering the system too late to be effectively utilized by the tissue. Thus, the lysine in these linkages would be at least partly unavailable. Other workers have shown that small quantities of isopeptides are found in the urine (14). 

FIGURE 27-41 Three-step cascade pathway by which ubiquitin is attached to a protein. Two different enzyme-ubiquitin intermediates are involved. The free carboxyl group of ubiquitin s carboxyl-terminal Gly residue is ultimately linked through an amide (isopeptide) bond to an e-amino group of a Lys residue of the target protein. Additional cycles produce polyubiquitin, a covalent polymer of ubiquitin subunits that targets the attached protein for destruction in eukaryotes. 

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... 

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