PROSITE documentation PDOC51858

PPPDE domain profile

Ubiquitin is a highly conserved 76-residue protein that is found in eukaryotes but not in bacteria and archaea. A wide variety of proteins are post-translationally modified by covalent attachment of a single or multiple molecule(s) of ubiquitin, a process called ubiquitination or ubiquitylation. Following the discovery of ubiquitin, a number of ubiquitin-like proteins have been found, including small ubiquitin-like modifiers (SUMOs), interferon-stimulated gene 15 (ISG15), neural precursor cell expressed, developmentally down regulated 8 (NEDD8), Autophygy 8 (Atg8), and Atg12. Conjugation of these modifiers to protein substrates occurs through sequential reactions that are performed by multiple enzymes. Protein ubiquitination is reversed by deubiquitinases (also known as deubiquitinylases) that cleave the isopeptide bond between ubiquitin and its target protein. Likewise, removal of ubiquitin-like proteins from the conjugated proteins is performed by structurally diverse isopeptidases, including deSUMOylases, deISGylases, and deNEDDylases, which cleave off SUMO, ISG15, and NEDD8 from the substrate proteins, respectively. The PPPDE (after Permutated Papain fold Peptidase of DsRNA viruses and Eukaryotes) domain is a cysteine isopeptidase that exhibits a deSUMOylase activity in PPPDE2 (DeSI-1) and a deubiquinating activity in PPPDE1 (DeSI-2). The PPPDE domain is restricted to eukaryotes, dsRNA viruses and one single stranded DNA virus [1,2,3,4].

The PPPDE domain can be described as a mixed α/β-fold composed of six β-strands and six α-helices. Five β-strands (β1-β5) form a highly curved central β-sheet that is stacked by a pair of antiparallel α-helices (α2 and α3) and surrounded by α1 and α4 (see <PDB:2WP7>). The PPPDE domain has a papain-like fold, in which a catalytic dyad is formed by a conserved N-terminal histidine residue on a β-strand (β2) and a conserved C-terminal cysteine residue on a following α-helix (α3) (the H-C configuration) as opposed to the C-H configuration seen in the classical papain-like peptidases. The sulfur atom of the Cys and the imidazole ring nitrogen of the His form a catalytic dyad in which the His can polarize the Cys to make it reactive [2].

Some proteins known to contain a PPPDE domain are listed below:

• Vertebrate DeSumoylating Isopeptidase 1 (DeSI-1) or PPPDE peptidase domain- containing protein 2 (PPPDE2), has isopeptidase but not SUMO-processing activity.
• Vertebrate DeSumoylating Isopeptidase 2 (DeSI-2) or PPPDE peptidase domain- containing protein 1 (PPPDE1), could mediate the ubiquitin chain editing of ribosomal protein S7 (RPS7), deubiquitinating Lys 48-linked ubiquitination, and stabilize RPS7 proteins.
• Schizosaccharomyces pombe DeSI-like protein sdu1, contains an ubiquitin C- terminal hydrolase activity which is involved in the defense against oxidative and nitrosative stresses [5].
• Fungal double-stranded (ds) RNA virus Cryphonectria hypovirus (CHV) polyproteins 3 and 4.
• Insect cypoviruses structural protein.
• Plant oryzavirus VP2 protein.
• Silk-moth single-stranded DNA parvo-like virus minor structural protein.

The profile we developed covers the entire PPPDE domain.