Structural and bioinformatics analysis of single-domain substrate-binding protein from Rhodothermus marinus

Substrate-binding proteins (SBPs) are key elements in determining the substrate specificity and high affinity of the ATP-binding cassette uptake system. A typical SBP has two domains that recognize substrates and are responsible for the specific substrate delivery. Conversely, in GenBank, genes for SBPs constituting a single domain SBP are often found in vicinity of a methyl-accepting chemotaxis protein gene. However, the molecular function and mechanism of single domain SBPs are not fully elucidated. To understand their molecular functions, we performed a crystallographic study of single domain SBP from Rhodothermus marinus (RmSBP). RmSBP crystals were soaked in solution containing NaBr or HgCl2 and their structures determined at 1.75 and 2.3 angstrom resolution, respectively. RmSBP soaked in NaBr exhibited disorder of the alpha 2-helix, beta 5-to beta 6-strand loop, and Cterminus region, showing the structural dynamic region of RmSBP. RmSBP soaked in HgCl2 showed that Hg2+ bound to Cys145 located between the alpha 5-and alpha 6-helices. The structural properties of RmSBP were compared with those of single domain SBP homologs. These results will contribute to continued identification of the molecular function and mechanism of single domain SBPs.