Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis.

Xiaoyuan He,Liqin Wang,Shuishu Wang

doi:10.1038/srep24442

Abstract

The transcriptional regulator PhoP is an essential virulence factor in Mycobacterium tuberculosis, and it presents a target for the development of new anti-tuberculosis drugs and attenuated tuberculosis vaccine strains. PhoP binds to DNA as a highly cooperative dimer by recognizing direct repeats of 7-bp motifs with a 4-bp spacer. To elucidate the PhoP-DNA binding mechanism, we determined the crystal structure of the PhoP-DNA complex. The structure revealed a tandem PhoP dimer that bound to the direct repeat. The surprising tandem arrangement of the receiver domains allowed the four domains of the PhoP dimer to form a compact structure, accounting for the strict requirement of a 4-bp spacer and the highly cooperative binding of the dimer. The PhoP-DNA interactions exclusively involved the effector domain. The sequence-recognition helix made contact with the bases of the 7-bp motif in the major groove, and the wing interacted with the adjacent minor groove. The structure provides a starting point for the elucidation of the mechanism by which PhoP regulates the virulence of M. tuberculosis and guides the design of screening platforms for PhoP inhibitors.

Highlights

The crystal structure of full-length PhoP reveals that it can form a symmetric RD dimer involving the α 4-β 5-α 5, with the DBDs of the dimer dangling by a disordered linker[16]
PhoP exists predominantly as a monomer in solution. These results led to the hypothesis that the phosphorylation of the RD promoted its dimerization and brought the two DBDs into close proximity to bind the DNA direct repeat[17]
The PhoP-DNA complex was crystallized as a 2:1 complex consisting of two molecules of PhoP bound to one DNA duplex containing a direct repeat[20]

Summary

Introduction

The crystal structure of full-length PhoP reveals that it can form a symmetric RD dimer involving the α 4-β 5-α 5, with the DBDs of the dimer dangling by a disordered linker[16]. PhoP exists predominantly as a monomer in solution These results led to the hypothesis that the phosphorylation of the RD promoted its dimerization and brought the two DBDs into close proximity to bind the DNA direct repeat[17]. This hypothesis appears to be consistent with the structure of the Escherichia coli KdpE-DNA complex[18] and the Klebsiella pneumoniae PmrA-DNA complex[19], which are currently the only available structures of full-length RR-DNA complexes in the OmpR/PhoB family. The mechanism underlying DNA sequence recognition likely applies to related transcriptional regulators

Methods

Results

Conclusion