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Fig. 8 | Biology Direct

Fig. 8

From: Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site

Fig. 8

Phylogenetic tree of M28-type sequences with known structures and sequences of the GPAA1 family. The evolutionary history was inferred by using the Maximum Likelihood method and JTT matrix-based model [70]. The tree with the highest log likelihood (− 15093.41) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the JTT model, and then selecting the topology with superior log likelihood value. This analysis involved 26 amino acid sequences. Evolutionary analyses were conducted in MEGA X [69]. For each leave of the phylogenetic tree, we list (i) a color code, (ii) the taxonomic abbreviation, (iii) the accession number from the protein data bank RCSB or UniProt, (iv) the sequence segment from the original sequence used for the alignment behind the tree, (v) the sequence length of the sequence segment and (vi) the molecular function code (AM aminopeptidase, CP carboxypeptidase, CT cyclotransferase, CTI cyclotransferase type I, CTII cyclotransferase type II). The sequence groups presented in the phylogenetic tree are (i) known two zinc-binding 3D structures 3fec [61], 1zbl [59], 4twe [64], 5ib9, 6hc6, 3iib, 1tkj, 1amp [28], 5gne [65], and 6esl [66] color-coded red; (ii) known single zinc-binding 3D structures 49fu [30], 4mhn, 4fai [30], 3pb4 [62], 2afo [60], 3si1 [63], 6qql, 3tc8, and 4fuu color-coded green as well as (iii) six sequences from the GPAA1 family color-coded blue. We show also the position of 3gux in the tree although it is not known how many zinc ions it does bind in the catalytic cleft (we predict one) as it was part of the alignment in Figure 1 of reference [23]. To note, there is no scientific article available for structures without listed reference above

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