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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
Feb 28, 2023 Vol.46 No.2, pp. 69~129
COVER PICTURE
The bulk tissue is a heterogeneous mixture of various cell types, which is depicted as a skein of intertwined threads with diverse colors each of which represents a unique cell type. Single-cell omics analysis untangles efficiently the skein according to the color by providing information of molecules at individual cells and interpretation of such information based on different cell types. The molecules that can be profiled at the individual cell by single-cell omics analysis includes DNA (bottom middle), RNA (bottom right), and protein (bottom left). This special issue reviews single-cell technologies and computational methods that have been developed for the single-cell omics analysis and how they have been applied to improve our understanding of the underlying mechanisms of biological and pathological phenomena at the single-cell level.

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