diff --git a/tests/fixtures/test_elm.json b/tests/fixtures/test_elm.json index 8bd3d951..b2c1a2c1 100644 --- a/tests/fixtures/test_elm.json +++ b/tests/fixtures/test_elm.json @@ -10,13 +10,13 @@ "ELME000351", "N-degron", "The N-end rule pathway regulates protein stability by targeting proteins for ubiquitin-dependent proteasomal degradation. Polyubiquitylation of N-end rule substrates depends on their recognition by N-recognins, specific E3 ubiquitin ligases that use their conserved UBR-box and N-box domains to bind specific N-terminal protein motifs, called N-degrons, in their target proteins. N-degrons are defined by a destabilizing N-terminal residue. Type I destabilizing residues can either occur as primary destabilizing residues, which are positively charged amino acids directly recognized by N-recognins, or as secondary and tertiary destabilizing amino acids, which can be conjugated to a primary destabilizing residue. N-degrons containing type I destabilizing residues are specifically bound by the UBR-box of N-recognins. In contrast, type II destabilizing residues, which comprise bulky hydrophobic amino acids, initiate protein degradation by binding to the N-box of N-recognins.", - "This class of N-degrons is defined by a positively charged type I primary destabilizing Arg or Lys residue in the N-terminal position, which is recognized by the UBR-box of N-recognins. Functional N-degrons of this class are generated from pre-N-degrons either by excision of the N-terminal Met on nascent proteins or by internal cleavage of a protein (Varshavsky,2011; Tasaki,2007). However, known Met-aminopeptidases catalyzing the N-terminal Met excision were so far found to cleave N-terminal of small amino acids (Varshavsky,2011), and the Arg- or Lys-containing N-degrons identified to date are generated by internal cleavage. It is important to note that the ELM prediction tool will only return internal N-degrons if the sequence of the cleavage product is entered for analysis.Once the active N-degron is generated, the N-terminal Arg or Lys residue binds to the UBR-box of N-recognins. The UBR-box is a highly conserved region whose tertiary structure is stabilized by two zinc fingers, which form a negatively charged binding pocket that rigidly binds the positively charged N-terminal amino acid. It was shown that Arg is favored over Lys as N-terminal residue. Binding also involves a shallow hydrophobic binding pocket that interacts with the side chain of the second residue of the motif. Despite a preference for hydrophobic residues in this second position, any amino acid except Pro is allowed. In addition, the UBR-box forms hydrogen bonds with the free alpha amino group and the backbone of the first three residues (Choi,2010; Tasaki,2012). Hence, the first two residues are the main determits for specific binding to the UBR-box (3NIH; 3NII; 3NIJ; 3NIM). Recent studies showed binding of N-terminal His-containing N-degrons to the UBR-box, indicating a possible role for His as a primary type I destabilizing residue. However, compared to other primary type I interactions, this binding is very weak and naturally occurring N-degrons containing His have not yet been identified (Choi,2010).", + "This class of N-degrons is defined by a positively charged type I primary destabilizing Arg or Lys residue in the N-terminal position, which is recognized by the UBR-box of N-recognins. Functional N-degrons of this class are generated from pre-N-degrons either by excision of the N-terminal Met on nascent proteins or by internal cleavage of a protein (Varshavsky,2011; Tasaki,2007). However, known Met-aminopeptidases catalyzing the N-terminal Met excision were so far found to cleave N-terminal of small amino acids (Varshavsky,2011), and the Arg- or Lys-containing N-degrons identified to date are generated by internal cleavage. It is important to note that the ELM prediction tool will only return internal N-degrons if the sequence of the cleavage product is entered for analysis.Once the active N-degron is generated, the N-terminal Arg or Lys residue binds to the UBR-box of N-recognins. The UBR-box is a highly conserved region whose tertiary structure is stabilized by two zinc fingers, which form a negatively charged binding pocket that rigidly binds the positively charged N-terminal amino acid. It was shown that Arg is favored over Lys as N-terminal residue. Binding also involves a shallow hydrophobic binding pocket that interacts with the side chain of the second residue of the motif. Despite a preference for hydrophobic residues in this second position, any amino acid except Pro is allowed. In addition, the UBR-box forms hydrogen bonds with the free alpha amino group and the backbone of the first three residues (Choi,2010; Tasaki,2012). Hence, the first two residues are the main determinants for specific binding to the UBR-box (3NIH; 3NII; 3NIJ; 3NIM). Recent studies showed binding of N-terminal His-containing N-degrons to the UBR-box, indicating a possible role for His as a primary type I destabilizing residue. However, compared to other primary type I interactions, this binding is very weak and naturally occurring N-degrons containing His have not yet been identified (Choi,2010).", "DEG_Nend_Nbox_1 DEG_Nend_UBRbox_1 DEG_Nend_UBRbox_2 DEG_Nend_UBRbox_3 DEG_Nend_UBRbox_4", "^M{0,1}[RK][^P].", "0.0002064", "Eukaryota", "zf-UBR (PF02207) Putative zinc finger in N-recognin (UBR box) (Stochiometry: 1 : 1)", - "KV", + "nan", "1", "3", "False",