6NZ4

YcjX-GDP (type I)

Summary for 6NZ4

• Entry DOI: 10.2210/pdb6nz4/pdb
• Descriptor: YcjX Stress Protein, GUANOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: g-protein, signaling protein
• Biological source: Shewanella oneidensis (strain MR-1)
• Total number of polymer chains: 2
• Total formula weight: 109802.36

Authors

Lee, S.,Tsai, J.,Tsai, F.T. (deposition date: 2019-02-12, release date: 2019-09-18, Last modification date: 2024-03-13)

Primary citation

Tsai, J.T.,Sung, N.,Lee, J.,Chang, C.,Lee, S.,Tsai, F.T.F.
Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.
J.Mol.Biol., 431:3179-3190, 2019

PubMed 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, ClpB, 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. Here, 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). 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, we show 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.

PubMed: 31202886
DOI: 10.1016/j.jmb.2019.06.006

Experimental method

X-RAY DIFFRACTION (1.92 Å)