Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein

Tsai, Joshua T.; Sung, Nuri; Lee, Jungsoon; Chang, Changsoo; Lee, Sukyeong; Tsai, Francis T. F.

doi:10.1016/j.jmb.2019.06.006

Title: Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein

Abstract

Stress proteins promote cell survival by monitoring protein homeostasis in cells and organelles. YcjX is a conserved protein of unknown function, which is highly upregulated in response to acute and chronic stress. Notably, heat shock induction of ycjX exceeded even levels observed for major stress-induced chaperones, including GroEL, CIpB, and HtpG, which use ATP as energy source. YcjX features a Walker-type nucleotide binding domain indicating that YcjX might function as a molecular chaperone. In this paper, we present the first crystal structure of YcjX from Shewanella oneidensis solved at 1.9-Å resolution by SAD phasing. We show that YcjX is a GTP-binding protein that shares at its core the canonical alpha-beta domain of p21^ras (Ras). However, unlike Ras, YcjX features several unique insertions, including an entirely α-helical domain not previously observed in Ras-like GTPases. We note that this helical domain is reminiscent of a similar domain in the Gα subunit of heterotrimeric G proteins, supporting a potential role for YcjX as a signal transducer of stress responses. To elucidate the mechanism of GTP hydrolysis, we determined crystal structures of YcjX bound to GDP and GDPCP, respectively, which crystallized in three different nucleotide switch conformations. Supported by targeted mutagenesis experiments, our studymore »« less

Authors:

Tsai, Joshua T. ^[1]; Sung, Nuri ^[1]; Lee, Jungsoon ^[1]; Chang, Changsoo ^[2]; Lee, Sukyeong ^[1]; Tsai, Francis T. F. ^[3]

Bayer College of Medicine, Houston, TX (United States). Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology
Argonne National Lab. (ANL), Argonne, IL (United States). Biosciences Division, Structural Biology Center
Bayer College of Medicine, Houston, TX (United States). Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology, Dept. of Molecular and Cellular Biology, and Dept. of Molecular Virology and Microbiology

Publication Date:: Fri Aug 09 00:00:00 EDT 2019

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Org.:: Baylor College of Medicine, Houston, TX (United States); National Institutes of Health (NIH); Welch Foundation, Houston, TX (United States); USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1570237

Alternate Identifier(s):: OSTI ID: 1775964

Grant/Contract Number:: AC02-06CH11357

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Molecular Biology

Additional Journal Information:: Journal Volume: 431; Journal Issue: 17; Journal ID: ISSN 0022-2836

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; G-protein; Ras; GRPase; stress signaling

Citation Formats


                    Tsai, Joshua T., Sung, Nuri, Lee, Jungsoon, Chang, Changsoo, Lee, Sukyeong, and Tsai, Francis T. F. Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.  United States: N. p., 2019. 
Web.  doi:10.1016/j.jmb.2019.06.006.

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                    Tsai, Joshua T., Sung, Nuri, Lee, Jungsoon, Chang, Changsoo, Lee, Sukyeong, & Tsai, Francis T. F. Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.  United States.  https://doi.org/10.1016/j.jmb.2019.06.006

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                    Tsai, Joshua T., Sung, Nuri, Lee, Jungsoon, Chang, Changsoo, Lee, Sukyeong, and Tsai, Francis T. F. Fri .  
"Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein".  United States.  https://doi.org/10.1016/j.jmb.2019.06.006.  https://www.osti.gov/servlets/purl/1570237.

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@article{osti_1570237,

  title        = {Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein},

  author       = {Tsai, Joshua T. and Sung, Nuri and Lee, Jungsoon and Chang, Changsoo and Lee, Sukyeong and Tsai, Francis T. F.},

  abstractNote = {Stress proteins promote cell survival by monitoring protein homeostasis in cells and organelles. YcjX is a conserved protein of unknown function, which is highly upregulated in response to acute and chronic stress. Notably, heat shock induction of ycjX exceeded even levels observed for major stress-induced chaperones, including GroEL, CIpB, and HtpG, which use ATP as energy source. YcjX features a Walker-type nucleotide binding domain indicating that YcjX might function as a molecular chaperone. In this paper, we present the first crystal structure of YcjX from Shewanella oneidensis solved at 1.9-Å resolution by SAD phasing. We show that YcjX is a GTP-binding protein that shares at its core the canonical alpha-beta domain of p21ras (Ras). However, unlike Ras, YcjX features several unique insertions, including an entirely α-helical domain not previously observed in Ras-like GTPases. We note that this helical domain is reminiscent of a similar domain in the Gα subunit of heterotrimeric G proteins, supporting a potential role for YcjX as a signal transducer of stress responses. To elucidate the mechanism of GTP hydrolysis, we determined crystal structures of YcjX bound to GDP and GDPCP, respectively, which crystallized in three different nucleotide switch conformations. Supported by targeted mutagenesis experiments, our study shows that YcjX utilizes a non-canonical switch 2' motif not previously observed in Ras-like GTPases. Together, our structures provide atomic snapshots of YcjX in different functional states, illustrating the structural determinants for stress signaling.},

  doi          = {10.1016/j.jmb.2019.06.006},

  journal      = {Journal of Molecular Biology},

  number       = 17,

  volume       = 431,

  place        = {United States},

  year         = {Fri Aug 09 00:00:00 EDT 2019},

  month        = {Fri Aug 09 00:00:00 EDT 2019}

}

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Figures / Tables:

Fig. 1: YcjX is a monomeric GTP hydrolase. (a) Organization of the ycjXF gene cluster in gram-negative bacteria. (b) Analytical size-exclusion chromatogram shows that YcjX is a 58.3-kDa monomer in solution. (c) YcjX hydrolyzes GTP but not ATP and requires magnesium ions for catalysis. Averages of three independent measurements (nmore »

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