Crystal Structure of Halophilic Dodecin: A Novel, Dodecameric Flavin Binding Protein from Halobacterium salinarum

Archaea obtained their name from their natural habitat, which reminds of the early earth surface. Among the extreme phenotypes within these entity, halophilic archaea exhibit adaption to high salt environment. Consequently these organisms are found under salt concentrations where they have to keep the osmolar balance by an salt-in-strategy. The uptake of salt in high amounts forces basic strategies of the cellular components to resist this otherwise denaturing environment.

Dodecin is a dodecameric, hollow-sphere arranged flavoprotein in the cytosol of Halobacterium salinarum. A single protein consists of 68 amino acid residues representing the smallest flavoprotein known to date. Of particular structural interest is the aromatic tetrade, which contains two π-stacked flavins covered by two tryptophans of the adjacent monomers.

Fig. 1: View along the threefold axis of the protein. α-Helices are coloured in red, β-sheets in blue, loops are orange, chloride ions in black and sodium ions in grey. Four trimers are arranged in a dodecamer of 23-cubic symmetry. The inner compartment of dodecin is enclosed by a protein shell. A β-sheet network forms the hollow-sphere and the α-helices are exposed to the bulk water. Entry into the inner compartment can only occur through channels, which are plugged by chloride ions. The yellow rectangle highlights one of the six aromatic tetrades in the dodecin molecule.

Of particular structural interest is the aromatic tetrade, which contains two π-stacked flavins covered by two tryptophans of the adjacent monomers.

The binding motif, allowing α-stacking interaction within this aromatic tetrade, is unique in the world of proteins and a radical deviation of all flavin binding mechanisms known to date. Dodecin binds its cofactor in a fundamentally different manner via the isoalloxazine ring. This structural particularity raises the question as to a functional potential, which is interesting with respect to the wide range of functions flavoproteins can perform. In addition, the character of π-stacking in this sandwich-like arrangement implies a high substrate tolerance of this binding type. The protein envelope may be able to readily accommodate other aromatic systems which are similar to the tricyclic isoalloazine ring and has led to the idea that dodecin may act as a kind of shuttle system for biological active compounds.

Fig. 2: Detailed view on the aromatic tetrade (highlighted in Fig. 1). The four aromatic ring sytems are placed in a distance of 3.2 Å. In this co-planar arrangement of four aromatic systems, the isoalloxazine-rings contact each other with the ribityl-chains pointing to the same direction towards the outer surface of the protein. This aromatic tetrade consisting of π-staggered indole groups of tryptophan W36 and the isoalloxazine-ring of flavins dominates the interaction between the trimers. The dominant polar interactions to the aromatic system are two hydrogen bonds of the amide side chain of Q55 (not shown).

References

  1. B. Bieger, L.-O. Essen, D. Oesterhelt, Structure, 2003, 11, 375-385

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