TOP

Research Article

Split Viewer

Mol. Cells 2013; 35(2): 158-165

Published online February 21, 2013

https://doi.org/10.1007/s10059-013-2303-z

© The Korean Society for Molecular and Cellular Biology

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

Ki-Woong Jeong, Hyunsook Ko, Sung-Ah Lee, Eunmi Hong, Sunggeon Ko, Hyun-Soo Cho, Weontae Lee, and Yangmee Kim

Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Institute of SMART Biotechnology, Konkuk University, Seoul 143-701, Korea, 1Department of Biochemistry, 2Department of Biology, Yonsei University, Seoul 120-749, Korea

Received: November 23, 2012; Revised: December 13, 2012; Accepted: December 17, 2012

Abstract

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-RRr) and a C-terminal effector domain (HP-RRe). 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-RRr and HP-RRe, T1, T2, heteronuclear NOE experiments have been performed and backbone dynamics of HP-RRr and HP-RRe were investigated. HP-RRr is a symmetric dimer and the interface region, ?4-?5-?5 of dimer, showed high rigidity (high S2 values). Site of rearrangements associated with phosphorylation of HP-RRr (Ser75: Rex = 3.382, Ile95: Rex = 5.228) showed slow che-mical exchanges. HP-RRe is composed of three ?-helices flanked on two sides by anti-parallel ?-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-RRe suggested that flexibility of HP-RRe is essential for interaction with DNA. In conclusion, backbone dynamics information for HP-RR implies that structural flexibilities in HP-RRr are necessary for the phosphorylation site and the dynamic nature of HP-RRe is essential for the regulation of interaction between protein and DNA.

Keywords backbone dynamics, C-terminal effector domain, HP1043 (HP-RR), NMR spectroscopy, N-terminal regulatory domain, spin relaxation

Article

Research Article

Mol. Cells 2013; 35(2): 158-165

Published online February 28, 2013 https://doi.org/10.1007/s10059-013-2303-z

Copyright © The Korean Society for Molecular and Cellular Biology.

Backbone Dynamics of an Atypical Orphan Response Regulator Protein, Helicobacter pylori 1043

Ki-Woong Jeong, Hyunsook Ko, Sung-Ah Lee, Eunmi Hong, Sunggeon Ko, Hyun-Soo Cho, Weontae Lee, and Yangmee Kim

Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Institute of SMART Biotechnology, Konkuk University, Seoul 143-701, Korea, 1Department of Biochemistry, 2Department of Biology, Yonsei University, Seoul 120-749, Korea

Received: November 23, 2012; Revised: December 13, 2012; Accepted: December 17, 2012

Abstract

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-RRr) and a C-terminal effector domain (HP-RRe). 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-RRr and HP-RRe, T1, T2, heteronuclear NOE experiments have been performed and backbone dynamics of HP-RRr and HP-RRe were investigated. HP-RRr is a symmetric dimer and the interface region, ?4-?5-?5 of dimer, showed high rigidity (high S2 values). Site of rearrangements associated with phosphorylation of HP-RRr (Ser75: Rex = 3.382, Ile95: Rex = 5.228) showed slow che-mical exchanges. HP-RRe is composed of three ?-helices flanked on two sides by anti-parallel ?-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-RRe suggested that flexibility of HP-RRe is essential for interaction with DNA. In conclusion, backbone dynamics information for HP-RR implies that structural flexibilities in HP-RRr are necessary for the phosphorylation site and the dynamic nature of HP-RRe is essential for the regulation of interaction between protein and DNA.

Keywords: backbone dynamics, C-terminal effector domain, HP1043 (HP-RR), NMR spectroscopy, N-terminal regulatory domain, spin relaxation

Mol. Cells
Nov 30, 2023 Vol.46 No.11, pp. 655~725
COVER PICTURE
Kim et al. (pp. 710-724) demonstrated that a pathogen-derived Ralstonia pseudosolanacearum type III effector RipL delays flowering time and enhances susceptibility to bacterial infection in Arabidopsis thaliana. Shown is the RipL-expressing Arabidopsis plant, which displays general dampening of the transcriptional program during pathogen infection, grown in long-day conditions.

Share this article on

  • line

Related articles in Mol. Cells

Molecules and Cells

eISSN 0219-1032
qr-code Download