Figure 1.
Workflow of the function prediction for the Tm1631 protein structure of unknown function.
Figure 2.
Tm1631 protein surface conservation analysis by ProBiS.
Tm1631 is shown in surface representation, which is colored by degrees of structural conservation from unconserved (white) to conserved (red). The predicted binding site is encircled by a yellow dashed line.
Figure 3.
Similar evolutionary patterns in nucleotide binding sites found in PDB using ProBiS.
Predicted Tm1631 binding site (left) is similar to (right): (a) active site in DNA binding site of polymerase X (2w9m) with DNA ligand that was transposed from homologous protein structure 3au6; (b) allosteric site in uridine monophosphate kinase (2jjx); (c) active site of DNA-glycosylase (3fhf) with DNA ligand transposed from homologous protein structure 3knt.
Table 1.
Top-ranked similar binding sites in proteins of different folds found using the predicted binding site in Tm1631 as query to the binding site comparison approach.a
Figure 4.
Tm1631-DNA model based on comparison of Tm1631 protein (1vpq) to known endonuclease IV-DNA complex (2nqj) from PDB.
Tm1631 is white, endonuclease IV is blue, DNA is green and light-blue cartoons, sulfate ions are CPK sticks, crescent-shaped grooves in both proteins are shaded areas. Initial Tm1631-DNA model; Tyr47 and Tyr48 penetrate the DNA's extra-helical region (left). Endonuclease IV-DNA complex (right).
Figure 5.
Tm1631-DNA model after 90 ns of MD.
Reactive phosphate group in DNA is marked with a red asterisk. (a) Tm1631-DNA model, residues that interact with the DNA are marked. (b) Magnified view of the Tm1631-DNA interface. DNA phosphate groups and residues that interact with the DNA are represented as sticks; black dashed lines denote putative hydrogen bonds and salt bridges. (c) and (d) Schematic picture of Tm1631-DNA and endonuclease IV-DNA interactions. Similar residues in Tm1631 and endonuclease IV binding sites are in white and blue ellipses, respectively. Hydrogen bonds with DNA are shown for amino acid side chains (solid black arrows) and backbone atoms (solid cyan arrows). Stacking interactions with DNA nucleotides are dashed black lines.