4ZKD

Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GDP and inorganic phosphate.

Summary for 4ZKD

• Entry DOI: 10.2210/pdb4zkd/pdb
• Descriptor: Superkiller protein 7, PHOSPHATE ION, GUANOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: gtpase, translation, ngd, ski, hydrolase, gtp-binding protein
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Cellular location: Cytoplasm : Q08491
• Total number of polymer chains: 1
• Total formula weight: 57220.95

Authors

Kowalinski, E.,Conti, E. (deposition date: 2015-04-30, release date: 2015-06-17, Last modification date: 2024-05-08)

Primary citation

Kowalinski, E.,Schuller, A.,Green, R.,Conti, E.
Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases.
Structure, 23:1336-1343, 2015

PubMed Abstract: Ski7 is a cofactor of the cytoplasmic exosome in budding yeast, functioning in both mRNA turnover and non-stop decay (NSD), a surveillance pathway that degrades faulty mRNAs lacking a stop codon. The C-terminal region of Ski7 (Ski7C) shares overall sequence similarity with the translational GTPase (trGTPase) Hbs1, but whether Ski7 has retained the properties of a trGTPase is unclear. Here, we report the high-resolution structures of Ski7C bound to either intact guanosine triphosphate (GTP) or guanosine diphosphate-Pi. The individual domains of Ski7C adopt the conformation characteristic of active trGTPases. Furthermore, the nucleotide-binding site of Ski7C shares similar features compared with active trGTPases, notably the presence of a characteristic monovalent cation. However, a suboptimal polar residue at the putative catalytic site and an unusual polar residue that interacts with the γ-phosphate of GTP distinguish Ski7 from other trGTPases, suggesting it might function rather as a GTP-binding protein than as a GTP-hydrolyzing enzyme.

PubMed: 26051716
DOI: 10.1016/j.str.2015.04.018

Experimental method

X-RAY DIFFRACTION (2.181 Å)