The detail of the interaction is exhibited in the zoom at right. On the left, the model obtained for umUPF1 structure was generated using the crystal 2XZL as template. The tightened conformation of umUPF1 is maintained by the interaction between the CH and RecA2 domains. For SMG1 and mTOR the important folds are Phosphatidylinositol 3-/4-kinase, the catalytic domain (IPR000403) in orange, an Armadillo-type fold (IPR016024) in Brown, the PIK-related kinase domain (IPR014009) in purple and in lila the FATC domain (IPR003152). For UPF3 the Nucleotide-binding alpha-beta plait domain (IPR012677) is shown in pink and the Regulator of nonsense-mediated decay UPF3 domain (IPR005120) in grey. In UPF2 the MIF4G-like and type 3 domains (IPR016021) are indicated in green and brown respectively and in lila the Up-frameshift suppressor 2 domain (IPR007193). Domain architectures according to InterPro and protein size are indicated. C) Domain structural analysis for UPF2, UPF3, and SMG1 (mTOR) in U. The score determined by STRING is also provided for each interaction. A solid line indicates a more reliable interaction. In both representations, blue lines join the two proteins involved in the interaction. UPF1 interaction with different proteins.Ī) Known protein interactions for hUPF1 using STRING. Putative NMD factors identified in Ustilago maydis. The main domain organization includes the UPF2-interacting domain which lies at the N-terminal region (IPR018999, light green) while the P-loop NTPase fold (IPR027417) was found towards the C-terminus in all species except for D. Five different predicted domains were found, showing different arrangements among the 32 species. Domain architectures and protein size according to InterPro are indicated at right for each species. The tree is drawn to scale and the evolutionary analysis was conducted using CLC sequence viewer. On the left side, the evolutionary history for UPF1 inferred using the UPGMA method is shown. The analysis involved 32 amino acidic sequences from animals, plants, fungi and protists. HTP corresponds to the number of records in which this modification site was assigned using only proteomic discovery-mode mass spectrometry.Įvolutionary relationship and domain structure of UPF1 in different species. (°) illustrates the positions where a Threonine in H. (*) indicates that the modification has been experimentally validated. The table at the bottom includes the sequence bearing either a phosphorylation (p) or ubiquitination (ub) site in H. The relative position for the different amino acids that could be modified in umUPF1 is shown on top. Post-translational modifications predicted for umUPF1. The glycine/serine-rich motif corresponds to the dark blue box. The loop 349–355 is highlighted in brown, which is interrupted in isoform 1 due to an intronic sequence. Conserved helicase motifs (I, II, II, IV, V and VI) are shown as gray boxes. Secondary structural elements are also depicted: rectangles represent α-helices and arrows correspond to β-sheets. Each domain is illustrated on top of the sequence using the same color code as in Fig 1. maydis.Īlignment of the full amino acid sequences for umUPF1 and hUPF1 where the conserved residues are indicated in blue. Positions for the human factor correspond to isoform 1 (Q92900-1). maydis is presented with a summary of the main features reported for the human factor. B) The relative position for each domain in both H. The amino acid position is shown for the beginning and the end of each peptide. Additional regulatory domains include domain 1B (orange) and domain 1C (red). The helicase region contains two RecA domains (yellow). The CH domain (green) is responsible for the interaction with UPF2, eRF1 and eRF3. UPF1 organization is very similar in Ustilago maydis and Homo sapiens.Ī) Schematic representation of the domain arrangement for UPF1 in Ustilago maydis (umUPF1) and Homo sapiens (hUPF1).
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