Summary for peptidase A28.001: DNA-damage inducible protein 1

Summary Alignment Tree Sequences Sequence features Distribution Structure Literature Inhibitors


MEROPS NameDNA-damage inducible protein 1
Other namesDDI1, Rings lost protein (Drosophila melanogaster), Rngo protein (Drosophila melanogaster), VSM1 g.p. (Saccharomyces cerevisiae)
Domain architecture
MEROPS Classification
Classification Clan AA >> Subclan (none) >> Family A28 >> Subfamily A >> A28.001
HolotypeDNA-damage inducible protein 1 (Saccharomyces cerevisiae), Uniprot accession P40087 (peptidase unit: 210-324), MERNUM MER0030084
History Identifier created: MEROPS 9.5 (1 July 2011)
Catalytic typeAspartic
NC-IUBMBNot yet included in IUBMB recommendations.
PreparationPreparation of Saccharomyces cerevisiae Ddi1 protein in a baculovirus system was described by Perteguer et al. (Perteguer et al., 2013).
Inhibitor commentsHIV proteinase inhibitors show different levels of inhibition in a complementation assay: Ddi1 variants from different organisms also show different levels of inhibition by these inhibitors (White et al., 2011). HIV proteinase inhibitors also inhibit recombinant enzyme (Perteguer et al., 2013).
StructureThe tertiary structure of the Ddi1 protein from Saccharomyces cerevisiae has been solved and the peptidase domain shows a fold very similar to that of retropepsin. The active form is a homodimer (Sirkis et al., 2006). The Asp-Gly-Thr-Ala motif around the active site aspartic acid is conserved between Ddi1 and retropepsins. The substrate binding groove in Ddi1 is wider allowing bulkier substrates to bind. Additional domains that flank the peptidase domain are involved in the binding of ubiquitinated substrates and the proteasome and Ddi1 is also known as a 'ubiquitin receptor'. There is an N-terminal ubiquitin-like (UBL) domain and a carboxy-terminal ubiquitin-associated (UBA)domain (Sirkis et al., 2006). The structure of the peptidase domain from human DDI1 has also been solved (PDB entry 3S8I).
Biological aspectsThe peptidase domain (RVP) is required for dimerization and the ubiquitin-like and ubiquitin-associated domains are required for checkpoint regulation, including rescue of the pds1-128 checkpoint mutant, and enrichment of GFP-Ddi1 in the nucleus. Mutation of the active site Asp220 abolishes rescue of the pds1-128 mutant, but has no effect on dimerization. The UBA domain is important for t-SNARE binding and undergoes phosphorylation on Thr346 and Thr348 (Gabriely et al., 2008). Ddi1 is involved in the turnover of a number of proteins including the the F-box protein Ufo1. F-box proteins bind the core SCF components of the E3 ubiquitin-protein ligases, which in turn control the cell cycle and cyclin degradation. Ufo1 is unique in containing a domain with multiple ubiquitin-interacting motifs, with which it interacts with Ddi1, but only when Ufo1 is ubiquitinated. Deleting these motifs increases the stability of Ufo1 and arrests the cell cycle (Ivantsiv et al., 2006). Ubiquitinated endonuclease Ho also binds Ddi1 and is then exported from the nucleus to the cytoplasm where the complex binds to and is degraded by the proteasome. Ho is important for switching between yeast mating types (Kaplun et al., 2005). Another binding partner and potential substrate of Ddi1 is Pho81p, which is an inhibitor of the cyclin-cyclin-dependent kinase (CDK) complex Pho80p-Pho85p. Ddi1 and Rad23p probably cooperative as negative regulators in the PHO pathway, which regulates expression of phosphate-responsive genes such as PHO5 encoding repressible acid phosphatase (Auesukaree et al., 2008).
KnockoutDdi1 was initailly identified as a negative regulator of constitutive exocytosis, because gene disruption leads to increased protein secretion (Lustgarten & Gerst, 1999; White et al., 2011).
Pharmaceutical relevanceThe enzyme from Leishmania parasites (and perhaps others) may be potential drug targets. There is evidence that this enzyme is a target for HIV-proteinase inhibitors that are shown to reduce Leishmania infections (White et al., 2011)
Contributing authorsColin Berry, Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, UK