An artificially constructed dimer through deformation of a short zinc-binding loop

We have analyzed the crystal structure of the dimeric form of d-glycero-d-manno-heptose-1,7-bisphosphate phosphatase from Burkholderia thailandensis (BtGmhB), catalyzing the removal of the phosphate at the 7 position of d-glycero-d-manno-heptose-1,7-bisphosphate. The crystal structure of BtGmhB revealed a dimeric form caused by a disruption of a short zinc-binding loop. The dimeric BtGmhB structure was induced by triggering the loss of Zn2+via the protonation of cysteine residues at pH 4.8 of the crystallization condition. Similarly, the addition of EDTA also causes the dimerization of BtGmhB. It appears there are two dimeric forms in solution with and without the disulfide bridge mediated by Cys95. The disulfide-free dimer produced by the loss of Zn2+ in the short zinc-binding loop is further converted to a stable disulfide-bonded dimer in vitro. Though the two dimeric forms are reversible, both of them are inactive due to a deformation of the active site. Single and triple mutant experiments confirmed the presence of two dimeric forms in vitro. Phosphatase assay results showed that only a zinc-bound monomeric form contains catalytic activity in contrast to the inactive zinc-free dimeric forms. The monomer-to-dimer transition caused by the loss of Zn2+ observed in this study is an example of reversal phenomenon caused by artificial proteins containing protein engineered zinc-finger motifs where the monomer-to-dimer transitions occurred in the presence of Zn2+. Therefore, this unusual dimerization process may be applicable to designing proteins possessing a short zinc-binding loop with a novel regulatory role. [Display omitted] •The loss of Zn2+ in a zinc-binding loop triggers artificial dimerization of BtGmhB.•The loss of Zn2+ disrupts the active site and thus inactivates catalytic activity.•The unusual function of the zinc-binding loop was confirmed by a mutant BpGmhB.•This unusual dimerization process may be applicable to design a noble PPI motif.