Figure 2

Structural alignment of the amino acid sequences of TrmI proteins with known three-dimensional structures using JOY[52]. Solvent inaccessible residues in the monomer are shown in upper-case letters. Residues belonging to α-helices, β-strands and 3-10 helices are shown in red, blue and maroon, respectively. The consensus secondary structure and its numbering in _TmTrmI (PDB sequence, residue 79 is missing) is shown underneath and above the sequences, respectively. In addition, numbering for each protein (PDB sequence) is indicated on the left of the sequence. Residues with positive phi torsion angle are shown in italic and cis peptide by a breve over the amino acid concerned. Residues that hydrogen bond to main-chain amide and to main-chain carbonyl are indicated in bold and underlined characters, respectively. Hydrogen bond to other side chain is indicated by a tilde (~) over the amino acid concerned. Residues involved in salt bridges at the dimeric and tetrameric interfaces are enclosed in pink and green squares, respectively. The cysteines of _PaTrmI, which are involved in inter-monomer disulfide bridges, are indicated by a star. The secondary structure elements are labeled according to the nomenclature defined by Schluckebier et al. [54]. For the C-terminal catalytic domain, β-strands and α-helices are associated with numbers and letters, respectively, whereas the reverse is used for the N-terminal auxiliary domain.