Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases

Abstract

The life cycles of retroviruses rely on the limited proteolysis catalyzed by the viral protease. Numerous eukaryotic organisms also express endogenously such proteases, which originate from retrotransposons or retroviruses, including DNA damage-inducible 1 and 2 (Ddi1 and Ddi2, respectively) proteins. In this study, we performed a comparative analysis based on the structural data currently available in Protein Data Bank (PDB) and Structural summaries of PDB entries (PDBsum) databases, with a special emphasis on the regions involved in dimerization of retroviral and retroviral-like Ddi proteases. In addition to Ddi1 and Ddi2, at least one member of all seven genera of the Retroviridae family was included in this comparison. We found that the studied retroviral and non-viral proteases show differences in the mode of dimerization and density of intermonomeric contacts, and distribution of the structural characteristics is in agreement with their evolutionary relationships. Multiple sequence and structure alignments revealed that the interactions between the subunits depend mainly on the overall organization of the dimer interface. We think that better understanding of the general and specific features of proteases may support the characterization of retroviral-like proteases.

Functional Study of the Retrotransposon-Derived Human PEG10 Protease

“…In addition, the D-S-G-A active site motif of human PR PEG10 is also identical to that of human Ddi1 and Ddi2 PRs, but this consensus motif is followed by a Ser residue (D-S-G-A-S) in PR PEG10 (Figure 1). Ser in this position is not characteristic of retroviral or Ddi1/Ddi2 PRs [29] but can be found in the Ty1 retrotransposon PR [30]. The D-T/S-G-A active site motif of most retroviral PRs is followed by an Asp residue, but in contrast with this Asp residue, a Ser in this position does not enable salt-bridge formation between PR PEG10 subunits.…”

“…Based on the results of secondary structure prediction and homology modeling, PR PEG10 shares its overall fold with those of retroviral PRs (Figure 2). PR PEG10 was found to show the highest sequence and structural similarity with DNA-damage-inducible 2 (Ddi2) and Ddi1 PRs [22,27,28]; each of these retroviral-like PRs contains an additional helical insert and has a six-stranded dimer interface organization, which was not found to be characteristic of retroviral PRs [29]. In addition, the D-S-G-A active site motif of human PR PEG10 is also identical to that of human Ddi1 and Ddi2 PRs, but this consensus motif is followed by a Ser residue (D-S-G-A-S) in PR PEG10 (Figure 1).…”

“…The D-T/S-G-A active site motif of most retroviral PRs is followed by an Asp residue, but in contrast with this Asp residue, a Ser in this position does not enable salt-bridge formation between PR PEG10 subunits. In the sequence motif of the consensus helix, retroviral PRs (excepting spumaretrovirus PRs) contain the G-R-N motif, but similarly to Ddi1 and Ddi2 proteins, PR PEG10 also contains a different sequence (G-V-R) in this helix, and thus lacks the corresponding interactions that are provided by the Arg residue of the G-R-N motif [29]. Structural analysis of retroviral and Ddi1 and Ddi2 PRs revealed correlation between the dimer interface organization and the intermonomeric contacts [29].…”

“…In the sequence motif of the consensus helix, retroviral PRs (excepting spumaretrovirus PRs) contain the G-R-N motif, but similarly to Ddi1 and Ddi2 proteins, PR PEG10 also contains a different sequence (G-V-R) in this helix, and thus lacks the corresponding interactions that are provided by the Arg residue of the G-R-N motif [29]. Structural analysis of retroviral and Ddi1 and Ddi2 PRs revealed correlation between the dimer interface organization and the intermonomeric contacts [29]. No data are available for in vitro dimer stability of PR PEG10 , but high structural similarity implies that its dimer stability may be comparable with those of Ddi1/Ddi2 PRs and may be lower than that of HIV-1 PR.…”

ER-Resident Transcription Factor Nrf1 Regulates Proteasome Expression and Beyond

“…Studies on yeast Ddi1 (yeast ortholog of DDI2) provided evidence for its proteolytic activity, which was found to be required for sufficient checkpoint regulation, and it also contributes to DNA replication stress response and to DNA-protein crosslink repair; however, very little is known regarding the physiological roles of DDI proteins in mammals [93][94][95]. Yeast Ddi1 contains UBL at the N-terminus and a UBA at the C-terminus.…”