title: Solution structure and tandem DNA recognition of the C-terminal effector domain of PmrA from Klebsiella pneumoniae.
abstract: Klebsiella pneumoniae PmrA is a polymyxin-resistance-associated response regulator. The C-terminal effector/DNA-binding domain of PmrA (PmrAC) recognizes tandem imperfect repeat sequences on the promoters of genes to induce antimicrobial peptide resistance after phosphorylation and dimerization of its N-terminal receiver domain (PmrAN). However, structural information concerning how phosphorylation of the response regulator enhances DNA recognition remains elusive. To gain insights, we determined the nuclear magnetic resonance solution structure of PmrAC and characterized the interactions between PmrAC or BeF3(-)-activated full-length PmrA (PmrAF) and two DNA sequences from the pbgP promoter of K. pneumoniae. We showed that PmrAC binds to the PmrA box, which was verified to contain two half-sites, 5'-CTTAAT-3' and 5'-CCTAAG-3', in a head-to-tail fashion with much stronger affinity to the first than the second site without cooperativity. The structural basis for the PmrAC-DNA complex was investigated using HADDOCK docking and confirmed by paramagnetic relaxation enhancement. Unlike PmrAC, PmrAF recognizes the two sites simultaneously and specifically. In the PmrAF-DNA complex, PmrAN may maintain an activated homodimeric conformation analogous to that in the free form and the interactions between two PmrAC molecules aid in bending and binding of the DNA duplex for transcription activation.
authors.affiliation: Institute of Biomedical Sciences, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Institute of Biochemistry and Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China.
authors.forename: Yuan-Chao
authors.initials: YC
authors.lastname: Lou
authors.forename: Iren
authors.initials: I
authors.lastname: Wang
authors.forename: M
authors.initials: M
authors.lastname: Rajasekaran
authors.forename: Yi-Fen
authors.initials: YF
authors.lastname: Kao
authors.forename: Meng-Ru
authors.initials: MR
authors.lastname: Ho
authors.forename: Shang-Te Danny
authors.initials: ST
authors.lastname: Hsu
authors.forename: Shan-Ho
authors.initials: SH
authors.lastname: Chou
authors.forename: Shih-Hsiung
authors.initials: SH
authors.lastname: Wu
authors.forename: Chinpan
authors.initials: C
authors.lastname: Chen
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D007711:Klebsiella pneumoniae / Q000235:genetics*; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017434:Protein Structure, Tertiary
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; C081902:pmrA protein, Bacteria