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

Published online February 28, 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
Sep 30, 2022 Vol.45 No.9, pp. 603~672
COVER PICTURE
The Target of Rapamycin Complex (TORC) is a central regulatory hub in eukaryotes, which is well conserved in diverse plant species, including tomato (Solanum lycopersicum). Inhibition of TORC genes (SlTOR, SlLST8, and SlRAPTOR) by VIGS (virus-induced gene silencing) results in early fruit ripening in tomato. The red/ orange tomatoes are early-ripened TORC-silenced fruits, while the green tomato is a control fruit. Top, left, control fruit (TRV2-myc); top, right, TRV2-SlLST8; bottom, left, TRV2-SlTOR; bottom, right, TRV2-SlRAPTOR(Choi et al., pp. 660-672).

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