Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution

Abstract

YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5 Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes.

Figure 1

Crystal structure of TmYeaZ (TM0874) from T. maritima. (a) Ribbon diagram of TmYeaZ monomer. Helices α1–α6 and β-strands β1–β9 are labeled. (b) A dimer of TmYeaZ consisting of two protomers in the asymmetric unit. (c) Alternate dimer formed by the crystallographic twofold axis. (d) Sequence alignment between TmYeaZ (PDB code 2a6a), EcYeaZ (PDB code 1okj) and StYeaZ (PDB code 2gel). The secondary structure and sequence numbering of TmYeaZ are shown in the top row. The secondary structure of StYeaZ is shown in the bottom row.

Figure 2

Structural comparisons of TmYeaZ and Kae1 (PDB code 2ivp). (a) Stereoview of the superposition of TmYeaZ (cyan) and Kae1 (red). (b) Superposition of the second domain of TmYeaZ (green) and the second domain of Kae1 (magenta). ATP bound to Kae1 is shown in stick representation.

Figure 3

Mapping of conserved regions onto the TmYeaZ structure. (a) Ribbon representation of TmYeaZ colored by sequence conservation of 237 homologs of TmYeaZ. The most conserved residues are shown in magenta and the least conserved residues in cyan. The most conserved regions of the structure are marked 1, 2 and 3, respectively. (b) Molecular surface of TmYeaZ colored by sequence conservation. The orientation of the molecule is the same as in Fig. 2 ▶(a). (c) A sequence logo representation of the three most conserved regions in YeaZ. A logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of the symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. (d, e) Molecular surface of the AB (d) and A ₂ (or B ₂) (e) dimers colored by sequence conservation, as in Figs. 1(b) and 1(c).

Figure 4

The conserved residues display large conformational flexibility. (a) Conserved residues on the potential binding surface of TmYeaZ (cyan) and StYeaZ (gray). The C^α positions of these residues are highlighted by spheres. The residues of StYeaZ are labeled in parentheses. (b) A stereoview of the unknown ligand (UNL; shown as red spheres) located between α1 and α2 of TmYeaZ (present in both monomers; the B monomer is shown here). The experimental density for the UNL (after solvent flattening and twofold averaging) is contoured at 1.5σ. Nearby protein residues are shown on stick representation.