Although RibU depends on ATP-binding domains for transport of riboflavin, its fold is much different from the ATP-binding site of ABC transporters. A search of the Protein Data Bank was run using DALI (distance matrix alignment), a fragment-based method that aligns structures based on successive hexapeptides, but this gave no structural homologues to RibU over its whole six transmembrane regions. In particular, no homologous membrane transporters were found. This implies that the protein structure and therefore mechanism is different to other transporters.
However some proteins did show limited structural similarity to RibU, for example to transmembrane regions 1-5. Five of the top seven similar entries are derived from particulate methane monooxygenase. This is an integral transmembrane protein with a 7-transmembrane helix A subunit and more information about it can be found at the European Bioinformatics Institute online database.
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| The structure of RibU (blue) overlaid with methane monooxygenase (orange) |
RibU homologues from eight bacterial species were sequenced and their pairwise sequence identity was found to be very close. This suggests the structure is conserved between species. The paper puts forward that ‘the highly conserved amino acids among these RibU homologues may be functionally important.’ The diagram below shows the regions where conserved amino acids are located. This shows that there are only a small number of conserved residues on the outer surface of RibU, whereas in the interior there is a large cluster of conserved amino acids.
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| Mapping of conserved amino acid residues based on sequence alignment of 12 RibU homologues. Residues conserved in 7-9 bacterial species are yellow and those conserved in 10-11 species are orange. Invariant residues are red. In b it can be seen that the riboflavin binding site contains highly-conserved residues. (Click for larger). |
Sequence alignment of RibU with other vitamin transporters (for example folate, thiamine precursor and cobalamin precursor) showed a conservation pattern very similar to the transmembrane regions of RibU, bringing up the possibility that the S components of other ECF transporters have a similar structure and membrane topology. This could potentially allow similar binding assays and structural studies on these transporters to be carried out.
Recognition, Binding and Transport of Riboflavin
Recognition, Binding and Transport of Riboflavin
