Figure 4

Amino acid alignments of putative atypical flexible arms in fungal tRNase Z^Ls. The top panel alignment shows putative atypical flexible arms found in certain fungal tRNase Z^Ls from Chaetomium globosum (CglTrz1), Myceliophthora thermophila (MthTrz1), Thielavia terrestris (TteTrz1), Y. lipolytica (YliTrz1), Microsporum canis (McaTrz1), Microsporum gypseum (MgyTrz1), Trichophyton rubrum (TruTrz1), Magnaporthe grisea (MgrTrz1), F. graminearum (FgrTrz1), Fusarium oxysporum (FoxTrz1), Fusarium verticillioides (FveTrz1), Nectria haematococca (NhaTrz1), Trichoderma atroviride (TatTrz1), Trichoderma virens (TviTrz1), Trichoderma reesei (TreTrz1), N. crassa (NcrTrz1), N. tetrasperma (NteTrz1), N. discreta (NdiTrz1), Podospora anserina (PanTrz1). The bottom panel alignment shows typical flexible arms found in tRNase Zs from B. subtilis (BsuTrz1) [55], S. cerevisiae (SceTrz1) [19], S. pombe (SpoTrz1) [14], D. melanogaster (DmeTrz1) [54] and H. sapiens (HsaTrz2) [9]. The predicted tRNase Z^Ls are defined in Additional file 1. The GP and Walker A-like motifs are indicated. Invariant and conserved amino acids are highlighted in Black and gray, respectively. The Asterisk indicates key residues in the D. Melanogaster tRNase Z^L that contribute to substrate binding [44]. The open circle denotes the residue in the D. Melanogaster tRNase Z^L that makes the largest contribution to substrate binding. Inverted triangles indicate the conserved glycine and proline residues in the GP motif, which are no longer conserved in certain fungal tRNase Z^Ls. Dark shading indicates identical residues, and gray shading designates conserved residues. Secondary structure assignment is based on the structure of the B. subtilis tRNase Z^S [34]. The secondary structures for α-helices, β-strands and 3₁₀-helix are indicated with Greek letters. Asterisks indicate key residues in the D. Melanogaster tRNase Z^L that contribute to substrate binding [44].