As mentioned before RibU is the S-component of the ECF transporter for Riboflavin in Staphylococcus aureus. RibU transports riboflavin from the periplasm into the cytoplasm of the host. Riboflavin binds to the periplasmic side of RibU about 5 Å into the surface of the periplasmic side. The riboflavin binding pocket itself is approximately 15 Å in width and 8 Å in thickness. The riboflavin binding pocket is made up of 13 conserved amino acids and is capped by the L1 loop.
RibU resembles a cylinder with rugged ends. The outer surface of the cylinder is predominantly hydrophobic (consistent with its membrane buried nature). In contrast to this the cytoplasmic and periplasmic surfaces have charged amino acids and it is positioned roughly perpendicular to the lipid membrane.
RibU is a homodimer and made of 6 trans-membrane segments.
RibU is split into 2 portions: 1 portion constitutes the trans-membrane segments 3 and 4, the other portion constitutes the other trans-membrane segments 1, 2, 5 and 6. Each of these trans-membrane segments is alpha-helix, where these alpha helices are connected via loop domains. One loop is of particular importance - the L1 loop. This is found above the substrate binding site on the periplasmic side of the membrane and allows the binding of the riboflavin substrate. The L1 loop connects the trans-membrane segments 1 and 2, where the second trans-membrane segment does not traverse the entire membrane. The L1 loop is made up of 17 amino acids of which 9 are highly conserved among RibU homologues in other bacterial species. See figure 2:
Sequence alignment and the Structural Fold
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| RibU transmembrane helices |
