Crystal structure of protein from Staphylococcus aureus

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Crystal structure of hypothetical protein from Staphylococcus aureus (1tsj) PDB entry 1tsj refers to a hypothetical protein of 139 residues which is predicted as both a dimer and a cytoplasmic protein. The protein is associated with Pfam entry PF06983 of 3-demethylubiquinone-9 3-methyltransferases. Among the sequence homologs found by PSI-Blast there are the predicted 3-demethylubiquinone-9 3-methyltransferase proteins Q192X9 from Desulfitobacterium hafniense and A9VFW6 from Bacillus weihenstephanensis. Its potential substrate is S-adenosyl-L-methionine with the formal charge +1. PDB entry 2rk9 was found to be structurally similar to 1tsj and share a significant sequence similarity of 21.0%. This structure homolog is an Oxidoreductase from Vibrio Splendidus and binds methylglyoxal which is not charged. Another structural similarity was found with PDB entry 1t47 which is a 4-hydroxyphenylpyruvate dioxygenase, but the sequence similarity is lower (7.7%). Fig. 1. Superimposition between chain A of 1tsj (orange) and chain B of 2rk9 (green). The arrow indicates the active site of 2rk9. Both the sequence and structure homologs are from the same superfamily titled 'Glyoxalase/bleomycin resistance protein/dioxygenase'. The Superimposition between chain A of 1tsj (orange) and chain B of 2rk9 (green) shows that the proteins indeed have similar folds (see Figure 1). It seems that the chosen active site of 1tsj is the largest cavity found on the protein's surface; in most cases this cavity is the functional area. Evidence approving this choice is that the superimpositions with 2rk9 placed its known active site at the same location. The electrostatic potential on the protein's surface is mostly negative (see Figure 2). The evolutionary conservation of 1tsj is shown in Figure 3. Fig. 2. The electrostatic potential of 1tsj. The figure was produced with Python Molecular Viewer. Fig.3 The evolutionary conservation of 1tsj. The figure was produced with ConSurf-DB. The potential substrate S-adenosyl-L-methionine has a positive formal charge which fits the negative electrostatic potential in the potential catalytic area. The alternative substrate found by the structural homology methylglyoxal is not charged and thus it's less probable that it will attach to the potential catalytic area. It seems more likely that 1tsj belongs to the Glyoxalase/bleomycin resistance protein/dioxygenase superfamily and functions as a demethylubiquinone-9 3-methyltransferase protein than that it functions as Oxidoreductase.

References

Created with the participation of Talya Etzion.

Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky