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; Yangmee Kim

doi:10.1007/s10059-013-2303-z

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, Yangmee Kim

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

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-RR ^r) and a C-terminal effector domain (HP-RR^e). 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-RR^r and HP-RR^e, T₁, T₂, heteronuclear NOE experiments have been performed and backbone dynamics of HP-RR^r and HP-RR ^e were investigated. HP-RR^r is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S ² values). Site of rearrangements associated with phosphorylation of HP-RR^r (Ser⁷⁵: R _ex = 3.382, Ile ⁹⁵: R _ex = 5.228) showed slow chemical exchanges. HP-RR^e is composed of three α-helices flanked on two sides by anti-parallel β-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-RR^e suggested that flexibility of HP-RR ^e is essential for interaction with DNA. In conclusion, backbone dynamics information for HP-RR implies that structural flexibilities in HP-RR^r are necessary for the phosphorylation site and the dynamic nature of HP-RR^e is essential for the regulation of interaction between protein and DNA.

Original language	English
Pages (from-to)	158-165
Number of pages	8
Journal	Molecules and cells
Volume	35
Issue number	2
DOIs	https://doi.org/10.1007/s10059-013-2303-z
Publication status	Published - 2013 Feb

Bibliographical note

Funding Information:
This work was supported by grants from the Basic Science Research Program (2011-0022873, Y. Kim), Priority Research Centers Program (2012-0006686, Y. Kim) through the National Research Foundation of Korea, funded by the Ministry of Education, Science, and Technology, and World Class University (WCU) program (R33-2009-000-10123-0, W. Lee).

All Science Journal Classification (ASJC) codes

Molecular Biology
Cell Biology

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@article{9ca2ecf631c840049f2e7e1eb7d35a82,

title = "Backbone dynamics of an atypical orphan response regulator protein, Helicobacter pylori 1043",

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-RR r) 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-RR e were investigated. HP-RRr is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S 2 values). Site of rearrangements associated with phosphorylation of HP-RRr (Ser75: R ex = 3.382, Ile 95: R ex = 5.228) showed slow chemical exchanges. HP-RRe is composed of three α-helices flanked on two sides by anti-parallel β-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-RR e 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.",

author = "Jeong, {Ki Woong} and Hyunsook Ko and Lee, {Sung Ah} and Eunmi Hong and Sunggeon Ko and Cho, {Hyun Soo} and Weontae Lee and Yangmee Kim",

note = "Funding Information: This work was supported by grants from the Basic Science Research Program (2011-0022873, Y. Kim), Priority Research Centers Program (2012-0006686, Y. Kim) through the National Research Foundation of Korea, funded by the Ministry of Education, Science, and Technology, and World Class University (WCU) program (R33-2009-000-10123-0, W. Lee).",

year = "2013",

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doi = "10.1007/s10059-013-2303-z",

language = "English",

volume = "35",

pages = "158--165",

journal = "Molecules and Cells",

issn = "1016-8478",

publisher = "Korean Society for Molecular and Cellular Biology",

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T1 - Backbone dynamics of an atypical orphan response regulator protein, Helicobacter pylori 1043

AU - Jeong, Ki Woong

AU - Ko, Hyunsook

AU - Lee, Sung Ah

AU - Hong, Eunmi

AU - Ko, Sunggeon

AU - Cho, Hyun Soo

AU - Lee, Weontae

AU - Kim, Yangmee

N1 - Funding Information: This work was supported by grants from the Basic Science Research Program (2011-0022873, Y. Kim), Priority Research Centers Program (2012-0006686, Y. Kim) through the National Research Foundation of Korea, funded by the Ministry of Education, Science, and Technology, and World Class University (WCU) program (R33-2009-000-10123-0, W. Lee).

PY - 2013/2

Y1 - 2013/2

N2 - 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-RR r) 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-RR e were investigated. HP-RRr is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S 2 values). Site of rearrangements associated with phosphorylation of HP-RRr (Ser75: R ex = 3.382, Ile 95: R ex = 5.228) showed slow chemical exchanges. HP-RRe is composed of three α-helices flanked on two sides by anti-parallel β-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-RR e 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.

AB - 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-RR r) 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-RR e were investigated. HP-RRr is a symmetric dimer and the interface region, α4-β5-α5 of dimer, showed high rigidity (high S 2 values). Site of rearrangements associated with phosphorylation of HP-RRr (Ser75: R ex = 3.382, Ile 95: R ex = 5.228) showed slow chemical exchanges. HP-RRe is composed of three α-helices flanked on two sides by anti-parallel β-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-RR e 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.

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