PDBsum entry 2hqo

Signaling protein

PDB id: 2hqo

Contents

Protein chains

119 a.a.

References listed in PDB file

Key reference

Title

Structure of an atypical orphan response regulator protein supports a new phosphorylation-Independent regulatory mechanism.

Authors

E.Hong, H.M.Lee, H.Ko, D.U.Kim, B.Y.Jeon, J.Jung, J.Shin, S.A.Lee, Y.Kim, Y.H.Jeon, C.Cheong, H.S.Cho, W.Lee.

Ref.

J Biol Chem, 2007, 282, 20667-20675. [DOI no: 10.1074/jbc.M609104200]

PubMed id

17491010

Abstract

Two-component signal transduction systems, commonly found in prokaryotes, typically regulate cellular functions in response to environmental conditions through a phosphorylation-dependent process. A new type of response regulator, HP1043 (HP-RR) from H. pylori, has been recently identified. HP-RR is essential for cell growth and does not require the well-known phosphorelay scheme. Unphosphorylated HP-RR binds specifically to its own promoter (P1043) and auto-regulates the promoter of the tlpB gene (PtlpB). We have determined the structure of HP-RR by NMR and X-ray crystallography, revealing a symmetrical dimer with two functional domains. The molecular topology resembles that of the OmpR/PhoB subfamily, however the symmetrical dimer is stable even in the unphosphorylated state. The dimer interface, formed by three secondary structure elements (a4-b5-a5), resembles that of the active, phosphorylated forms of ArcA and PhoB. Several conserved residues of the HP-RR dimeric interface deviate from the OmpR/PhoB subfamily, although there are similar salt bridges and hydrophobic patches within the interface. Our findings reveal how a new type of response regulator protein could function as a cell growth-associated regulator in the absence of post-translational modification.

Figure 3.
FIGURE 3. NMR structures of the DNA-binding domain and chemical shift mapping of the residues important for DNA binding. A, stereoview of the backbone traces from the final ensemble of 20 solution structures. The -helices are displayed in orange and -sheets in blue. B, electrostatic potential surface of the transactivation domain is displayed. Red, blue, and white colors represent negative, positive, and neutral electrostatic potential, respectively. The backside view of the molecule rotated by 180° around the vertical axis is also shown. Residues important for DNA binding are labeled. C, chemical shift change of the effector domain upon DNA binding. The chemical shift changes are calculated by using the equation: [tot] = (( [HN]W[HN])^2 + ( [N]W[N])^2)^1/2, where [i] is the chemical shift of nucleus i, and W[i] denotes its weight factor (W[HN] = 1, W[N] = 0.2). D, residues that exhibit significant chemical shift perturbation upon DNA binding. Magenta indicates [tot] > 0.2, and yellow indicates 0.1 < [tot] <0.2.

Figure 4.
FIGURE 4. X-ray structure and dynamics properties of the dimeric interface of the regulatory domain. A, structural comparison of the superimposed C[ ]atoms of HP-RR^r (yellow), the active ArcA^N (orange, PDB accession code 1XHF), and the active PhoB^N (green, PDB accession code 1ZES). Major structural deviations occur from a 4-amino acid deletion as shown within the blue circle. B, both electrostatic and hydrophobic interactions of the dimeric interface are shown. A network of ionic interactions is formed between Glu^83 ( 4), Asp^93 ( 5), and Arg^108 ( 5). The core interactions of the hydrophobic patch consisting of Val^84 ( 4), Phe^87 ( 4), Ala^104 ( 5), Ala^107 ( 5), and Ala^111 ( 5) are also shown between dimeric interface. C, dynamic properties of HP-RR^r.S^2 and R[ex] values are depicted. Order parameters, S^2, are colored onto the ribbon structure. According to increasing S^2, residues are colored from red (S^2 < 0.70) to yellow (S^2 > 0.90) in a linear fashion. For the residues with R[ex] > 0.5 s^-1, ribbon diameter (pink color) is increased in a linear fashion.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 20667-20675) copyright 2007.