PDBsum entry 4zkd

Gtp-binding protein

PDB id: 4zkd

Contents

Protein chain

470 a.a.

Ligands

PO4

GDP

Metals

_MG

Waters ×10

PDB id:

4zkd

Name:

Gtp-binding protein

Title:

Crystal structure of the s. Cerevisiae ski7 gtpase-like domain, bound to gdp and inorganic phosphate.

Structure:

Superkiller protein 7. Chain: a. Synonym: ski7. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ski7, yor076c, yor29-27. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.18Å R-factor: 0.219 R-free: 0.246

Authors:

E.Kowalinski,E.Conti

Key ref:

E.Kowalinski et al. (2015). Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases. Structure, 23, 1336-1343. PubMed id: 26051716 DOI: 10.1016/j.str.2015.04.018

Date:

30-Apr-15 Release date: 17-Jun-15

Protein chain

Q08491  (SKI7_YEAST) -  Superkiller protein 7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 747 a.a.

Struc: 470 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.str.2015.04.018

Structure 23:1336-1343 (2015)

PubMed id: 26051716

Saccharomyces cerevisiae Ski7 Is a GTP-Binding Protein Adopting the Characteristic Conformation of Active Translational GTPases.

E.Kowalinski, A.Schuller, R.Green, E.Conti.

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.