Backbone dynamics of an atypical orphan response regulator protein, Helicobacter pylori 1043

An atypical orphan response regulator protein, HP1043 (HP-RR) in Helicobacter pylori, is proven to be essential for cell growth and does not require the well known phosphorelay scheme. HP-RR was identified as a symmetric dimer with two functional domains, an N-terminal regulatory domain (HP-RR ^r) and a C-terminal effector domain (HP-RR^e). HP-RR is a new class of response regulator, as a phosphorylation-independent regulator. Previously, we have presented a detailed three-dimensional structure of HP-RR using NMR spectroscopy and X-ray crystallography. In this study, in order to understand the functional importance of flexibilities in HP-RR^r and HP-RR^e, T₁, T₂, heteronuclear NOE experiments have been performed and backbone dynamics of HP-RR^r and HP-RR ^e were investigated. HP-RR^r is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S ² values). Site of rearrangements associated with phosphorylation of HP-RR^r (Ser⁷⁵: R _ex = 3.382, Ile ⁹⁵: R _ex = 5.228) showed slow chemical exchanges. HP-RR^e is composed of three α-helices flanked on two sides by anti-parallel β-sheets. Low order parameters as well as conformational exchanges in the centers of loop regions known as the DNA binding site and transcription site of HP-RR^e suggested that flexibility of HP-RR ^e is essential for interaction with DNA. In conclusion, backbone dynamics information for HP-RR implies that structural flexibilities in HP-RR^r are necessary for the phosphorylation site and the dynamic nature of HP-RR^e is essential for the regulation of interaction between protein and DNA.