Abstract
Ubiquitination is important for numerous cellular processes in most eukaryotic organisms, including cellular proliferation, development, and protein turnover by the proteasome. The intestinal parasite Entamoeba histolytica harbors an extensive ubiquitin-proteasome system. Proteasome inhibitors are known to impair parasite proliferation and encystation, suggesting the ubiquitin-proteasome pathway as a viable therapeutic target. However, no functional studies of the E. histolytica ubiquitination enzymes have yet emerged. Here, we have cloned and characterized multiple E. histolytica ubiquitination components, spanning ubiquitin and its activating (E1), conjugating (E2), and ligating (E3) enzymes. Crystal structures of EhUbiquitin reveal a clustering of unique residues on the α1 helix surface, including an eighth surface lysine not found in other organisms, which may allow for a unique polyubiquitin linkage in E. histolytica. EhUbiquitin is activated by and forms a thioester bond with EhUba1 (E1) in vitro, in an ATP- and magnesium-dependent fashion. EhUba1 exhibits a greater maximal initial velocity of pyrophosphate:ATP exchange than its human homolog, suggesting different kinetics of ubiquitin activation in E. histolytica. EhUba1 engages the E2 enzyme EhUbc5 through its ubiquitin-fold domain to transfer the EhUbiquitin thioester. However, EhUbc5 has a >10-fold preference for EhUba1∼Ub compared with unconjugated EhUba1. A crystal structure of EhUbc5 allowed prediction of a noncovalent "backside" interaction with EhUbiquitin and E3 enzymes. EhUbc5 selectively engages EhRING1 (E3) to the exclusion of two HECT family E3 ligases, and mutagenesis indicates a conserved mode of E2/RING-E3 interaction in E. histolytica.
Highlights
Ubiquitination plays critical roles in many cellular processes
Crystal structures of EhUbiquitin reveal a clustering of unique residues on the ␣1 helix surface, including an eighth surface lysine not found in other organisms, which may allow for a unique polyubiquitin linkage in E. histolytica
Incomplete low-resolution data were manifested as unusually high R-factors and average B-factors during refinement (Table 2); the electron density was of good quality (Fig. 1B), with clear electron density obtained for the divergent residues of EhUbiquitin upon phasing by molecular replacement with human ubiquitin (PDB code 1UBQ)
Summary
Results: The Entamoeba histolytica ubiquitin activating, conjugating, and ligating enzymes interact and transfer ubiquitin. We have cloned and characterized multiple E. histolytica ubiquitination components, spanning ubiquitin and its activating (E1), conjugating (E2), and ligating (E3) enzymes. EhUba engages the E2 enzyme EhUbc through its ubiquitin-fold domain to transfer the EhUbiquitin thioester. ULM attachments are catalyzed by conserved enzyme cascades, with ATP-dependent ULM activation catalyzed by E1, conjugation by E2, and targeting of specific protein substrates by E3 ligases [3]. HECT family E3 enzymes possess a catalytic cysteine that accepts the ubiquitin thioester from bound E2ϳUb prior to ubiquitin isopeptide bond formation with a lysine acceptor [7]. More recent bioinformatic analyses of the E. histolytica genome revealed an extensive family of putative ubiquitin activating, conjugating, and ligating enzymes, as well as parallel systems for other ubiquitin-like modifiers [15]. We hypothesize that differences revealed between the E. histolytica components and well studied mammalian homologs may elucidate a potential means for specific targeting of ubiquitination within the parasitic amoeba
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