PDBsum entry 3ew2

Unknown function

PDB id: 3ew2

Contents

Protein chains

114 a.a.

121 a.a.

95 a.a.

Ligands

BTN ×7

Waters ×122

References listed in PDB file

Key reference

Title

Crystal structure of rhizavidin: insights into the enigmatic high-Affinity interaction of an innate biotin-Binding protein dimer.

Authors

A.Meir, S.H.Helppolainen, E.Podoly, H.R.Nordlund, V.P.Hytönen, J.A.Määttä, M.Wilchek, E.A.Bayer, M.S.Kulomaa, O.Livnah.

Ref.

J Mol Biol, 2009, 386, 379-390. [DOI no: 10.1016/j.jmb.2008.11.061]

PubMed id

19111749

Abstract

Rhizavidin, from the proteobacterium Rhizobium etli, exhibits high affinity towards biotin but maintains an inherent dimeric quaternary structure and thus, differs from all other known tetrameric avidins. Rhizavidin also differs from the other avidins, since it lacks the characteristic tryptophan residue positioned in the L7,8 loop that plays a crucial role in high-affinity binding and oligomeric stability of the tetrameric avidins. The question is, therefore, how does the dimer exist and how is the high biotin-binding affinity retained? For this purpose, the crystal structures of apo- and biotin-complexed rhizavidin were determined. The structures reveal that the rhizavidin monomer exhibits a topology similar to those of other members of the avidin family, that is, eight antiparallel beta-strands that form the conventional avidin beta-barrel. The quaternary structure comprises the sandwich-like dimer, in which the extensive 1-4 intermonomer interface is intact, but the 1-2 and 1-3 interfaces are nonexistent. Consequently, the biotin-binding site is partially accessible, due to the lack of the tryptophan "lid" that distinguishes the tetrameric structures. In rhizavidin, a disulfide bridge connecting the L3,4 and L5,6 loops restrains the L3,4 loop conformation, leaving the binding-site residues essentially unchanged upon biotin binding. Our study suggests that in addition to the characteristic hydrogen bonding and hydrophobic interactions, the preformed architecture of the binding site and consequent shape complementarity play a decisive role in the high-affinity biotin binding of rhizavidin. The structural description of a novel dimeric avidin-like molecule will greatly contribute to the design of improved and unique avidin derivatives for diversifying the capabilities of avidin-biotin technology.

Figure 3.
Fig. 3. Schematic ribbon presentation of the rhizavidin dimer. The monomers are labeled and shown in cyan and magenta, respectively, and the biotin molecules in the binding sites are shown in black. The disulfide bridges are shown in stick presentation and marked by arrows. In the rhizavidin dimer, the binding sites and the corresponding biotin carboxylates are located at opposite positions (approximately 180° rotation).

Figure 5.
Fig. 5. Biotin binding-site residues of the avidins. (a) Schematic representation of the hydrogen-bonding network in the rhizavidin, avidin, AVR4, and streptavidin complexes with biotin. In all four proteins, the biotin ring system forms an identical network of H-bond interactions. In all avidins, the L3,4 loop contributes a single H-bond interaction with one of the biotin ureido nitrogens. In rhizavidin, streptavidin, and AVR4, each of the biotin carboxylate oxygens forms a single H-bond interaction with residues at similar positions on the proteins. In this context, rhizavidin Gly49 from the L3,4 loop is positioned next to Cys50, which forms a disulfide bridge and contributes to the stability of the region upon biotin binding. In avidin, however, the biotin carboxylate oxygens form a more complex set of H-bonding interactions. (b) Aromatic residues involved in biotin binding in rhizavidin (middle), avidin (left), and streptavidin (right). The network of aromatic residues in avidin is identical with that in AVR4, which was thus not included. The additional Trp residue from an adjacent monomer is shown in magenta for avidin and streptavidin, and its absence is apparent in rhizavidin. The disulfide bridge in rhizavidin between Cys50 and Cys79 (shown in red) does not appear in other avidin structures but is located in an equivalent position as Phe72 of avidin and Phe70 of AVR4 (not shown). Streptavidin (right) lacks such an aromatic residue.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 386, 379-390) copyright 2009.