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What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor?

Michelle C, Vourc'h P, Mignon L, Andres CR - J. Mol. Evol. (2009)

Bottom Line: The subdivision of E2 into four classes did not correspond to the phylogenetic tree.When present, the active cysteine was found 7 to 8 amino acids from the C-terminal end of HPN.A better understanding of the functions of these enzymes is necessary to decipher several human diseases.

View Article: PubMed Central - PubMed

Affiliation: Faculté de Médecine, Génétique de l'Autisme et des Déficiences Mentales, INSERM U930, Université François Rabelais, 10, boulevard Tonnellé, BP 3223, 37032, Tours, France.

ABSTRACT
Ubiquitin (Ub)-conjugating enzymes (E2) are key enzymes in ubiquitination or Ub-like modifications of proteins. We searched for all proteins belonging to the E2 enzyme super-family in seven species (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Arabidopsis thaliana) to identify families and to reconstruct each family's phylogeny. Our phylogenetic analysis of 207 genes led us to define 17 E2 families, with 37 E2 genes, in the human genome. The subdivision of E2 into four classes did not correspond to the phylogenetic tree. The sequence signature HPN (histidine-proline-asparagine), followed by a tryptophan residue at 16 (up to 29) amino acids, was highly conserved. When present, the active cysteine was found 7 to 8 amino acids from the C-terminal end of HPN. The secondary structures were characterized by a canonical alpha/beta fold. Only family 10 deviated from the common organization because the proteins were devoid of enzymatic activity. Family 7 had an insertion between beta strands 1 and 2; families 3, 5 and 14 had an insertion between the active cysteine and the conserved tryptophan. The three-dimensional data of these proteins highlight a strong structural conservation of the core domain. Our analysis shows that the primitive eukaryote ancestor possessed a diversified set of E2 enzymes, thus emphasizing the importance of the Ub pathway. This comprehensive overview of E2 enzymes emphasizes the diversity and evolution of this superfamily and helps clarify the nomenclature and true orthologies. A better understanding of the functions of these enzymes is necessary to decipher several human diseases.

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Explanative structure showing in their 3D context the different residues mentioned in Fig. 6. Loops are labeled L1 to L8; β-strands are labeled S1 to S4; and helices are labeled H1 to H4 (with “h” for the generally conserved 3/10 helix). (Adapted from 3D structure of UBE2D2, PDB source E2SK, and legended from Winn et al. 2004)
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Fig1: Explanative structure showing in their 3D context the different residues mentioned in Fig. 6. Loops are labeled L1 to L8; β-strands are labeled S1 to S4; and helices are labeled H1 to H4 (with “h” for the generally conserved 3/10 helix). (Adapted from 3D structure of UBE2D2, PDB source E2SK, and legended from Winn et al. 2004)

Mentions: The general signature motif of the E2 enzyme superfamily is an HPN tripeptide (histidine–proline–asparagine) and an active cysteine residue generally located at the eighth amino acid on the C-terminal side of this canonical motif (Cottee et al. 2006) (Fig. 1). In addition, several domains are highly conserved and may play an important role in the function of these enzymes. For example, the sequence between the H2 helix and L3 loop seems to be the binding site for free or ligated Ub (Winn et al. 2004), whereas a highly conserved N-terminal sequence in the core domain may play a role in the interaction with E1 enzymes. To ascertain a high specificity, Ub binds to the target protein by way of a complex mechanism. Because the small number of E1 enzymes cannot allow for great specificity, the selection of the target protein has to come from the other enzymes. However, little is known about the relation between E2 and E3 enzymes. Although several E2 enzymes can interact with the same E3 enzyme, the converse is true as well: one unique E2 enzyme can work with several E3 enzymes as well RING and HECT enzymes. Abundant structural data exist about the interaction of E2 and E3 proteins, implicating the L4 and L7 loops as key sites of E3 interactions (Winn et al. 2004). However, although certain amino acid positions are clearly identified to play a role as sites for E3 binding, other elements on the E2 surface are required to define the specificity of the interaction of any given E2–E3 pair, such as polar contacts involving side chains in H1 helix of the E2 (Pickart 2001). Even if the phenylalanine in position 63 in the L4 loop is essential for HECT interaction and the tryptophan in position 95 in the L7 loop is necessary for RING interaction, it is the overall three-dimensional (3D) surface and charge that significantly contribute to the specificity of interaction with E3 enzymes (Martinez-Noel et al. 2001). In the same way, different E3 enzymes might have slightly different binding surfaces on a same E2 (Özkan et al.2005). Moreover, supplementary levels of regulation and specificity are mediated by the intervention of additional proteins.Fig. 1


What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor?

Michelle C, Vourc'h P, Mignon L, Andres CR - J. Mol. Evol. (2009)

Explanative structure showing in their 3D context the different residues mentioned in Fig. 6. Loops are labeled L1 to L8; β-strands are labeled S1 to S4; and helices are labeled H1 to H4 (with “h” for the generally conserved 3/10 helix). (Adapted from 3D structure of UBE2D2, PDB source E2SK, and legended from Winn et al. 2004)
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2691932&req=5

Fig1: Explanative structure showing in their 3D context the different residues mentioned in Fig. 6. Loops are labeled L1 to L8; β-strands are labeled S1 to S4; and helices are labeled H1 to H4 (with “h” for the generally conserved 3/10 helix). (Adapted from 3D structure of UBE2D2, PDB source E2SK, and legended from Winn et al. 2004)
Mentions: The general signature motif of the E2 enzyme superfamily is an HPN tripeptide (histidine–proline–asparagine) and an active cysteine residue generally located at the eighth amino acid on the C-terminal side of this canonical motif (Cottee et al. 2006) (Fig. 1). In addition, several domains are highly conserved and may play an important role in the function of these enzymes. For example, the sequence between the H2 helix and L3 loop seems to be the binding site for free or ligated Ub (Winn et al. 2004), whereas a highly conserved N-terminal sequence in the core domain may play a role in the interaction with E1 enzymes. To ascertain a high specificity, Ub binds to the target protein by way of a complex mechanism. Because the small number of E1 enzymes cannot allow for great specificity, the selection of the target protein has to come from the other enzymes. However, little is known about the relation between E2 and E3 enzymes. Although several E2 enzymes can interact with the same E3 enzyme, the converse is true as well: one unique E2 enzyme can work with several E3 enzymes as well RING and HECT enzymes. Abundant structural data exist about the interaction of E2 and E3 proteins, implicating the L4 and L7 loops as key sites of E3 interactions (Winn et al. 2004). However, although certain amino acid positions are clearly identified to play a role as sites for E3 binding, other elements on the E2 surface are required to define the specificity of the interaction of any given E2–E3 pair, such as polar contacts involving side chains in H1 helix of the E2 (Pickart 2001). Even if the phenylalanine in position 63 in the L4 loop is essential for HECT interaction and the tryptophan in position 95 in the L7 loop is necessary for RING interaction, it is the overall three-dimensional (3D) surface and charge that significantly contribute to the specificity of interaction with E3 enzymes (Martinez-Noel et al. 2001). In the same way, different E3 enzymes might have slightly different binding surfaces on a same E2 (Özkan et al.2005). Moreover, supplementary levels of regulation and specificity are mediated by the intervention of additional proteins.Fig. 1

Bottom Line: The subdivision of E2 into four classes did not correspond to the phylogenetic tree.When present, the active cysteine was found 7 to 8 amino acids from the C-terminal end of HPN.A better understanding of the functions of these enzymes is necessary to decipher several human diseases.

View Article: PubMed Central - PubMed

Affiliation: Faculté de Médecine, Génétique de l'Autisme et des Déficiences Mentales, INSERM U930, Université François Rabelais, 10, boulevard Tonnellé, BP 3223, 37032, Tours, France.

ABSTRACT
Ubiquitin (Ub)-conjugating enzymes (E2) are key enzymes in ubiquitination or Ub-like modifications of proteins. We searched for all proteins belonging to the E2 enzyme super-family in seven species (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Arabidopsis thaliana) to identify families and to reconstruct each family's phylogeny. Our phylogenetic analysis of 207 genes led us to define 17 E2 families, with 37 E2 genes, in the human genome. The subdivision of E2 into four classes did not correspond to the phylogenetic tree. The sequence signature HPN (histidine-proline-asparagine), followed by a tryptophan residue at 16 (up to 29) amino acids, was highly conserved. When present, the active cysteine was found 7 to 8 amino acids from the C-terminal end of HPN. The secondary structures were characterized by a canonical alpha/beta fold. Only family 10 deviated from the common organization because the proteins were devoid of enzymatic activity. Family 7 had an insertion between beta strands 1 and 2; families 3, 5 and 14 had an insertion between the active cysteine and the conserved tryptophan. The three-dimensional data of these proteins highlight a strong structural conservation of the core domain. Our analysis shows that the primitive eukaryote ancestor possessed a diversified set of E2 enzymes, thus emphasizing the importance of the Ub pathway. This comprehensive overview of E2 enzymes emphasizes the diversity and evolution of this superfamily and helps clarify the nomenclature and true orthologies. A better understanding of the functions of these enzymes is necessary to decipher several human diseases.

Show MeSH
Related in: MedlinePlus