4ZKD

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF21921	e4zkdA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PF21921	ECOD (1.6)
A	PF21920	e4zkdA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PF21920	ECOD (1.6)
A	PF00009	e4zkdA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00009	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
A	PF21921	Ski7 domain II (Ski7_2nd)	Ski7 domain II	This entry represents the Ski7 II domain, which is a component of the C-terminal region of the Ski7 protein in budding yeast. Ski7 is a cofactor of the cytoplasmic exosome that functions in mRNA turnover and non-stop decay (NSD). The Ski7 II domain s ...	This entry represents the Ski7 II domain, which is a component of the C-terminal region of the Ski7 protein in budding yeast. Ski7 is a cofactor of the cytoplasmic exosome that functions in mRNA turnover and non-stop decay (NSD). The Ski7 II domain shares overall sequence similarity with the translational GTPase (trGTPase) Hbs1, but unlike other trGTPases, Ski7 might function as a GTP-binding protein rather than a GTP-hydrolyzing enzyme. The Ski7C is organized into three domains, with domain I adopting the alpha beta fold of GTP-binding domains, and domains II and III each adopting the structure of a closed beta barrel. Domains II and III appear to form a single unit and interact with the G domain, and the three domains interact intra-molecularly not only via their globular folds but also via extended segments.	Domain
A	PF21920	Ski7 III domain (Ski7_3rd)	Ski7 III domain	This entry represents the Ski7 III domain, which is a component of the C-terminal region of the Ski7 protein in budding yeast. Ski7 is a cofactor of the cytoplasmic exosome that functions in mRNA turnover and non-stop decay (NSD). The Ski7 II domain ...	This entry represents the Ski7 III domain, which is a component of the C-terminal region of the Ski7 protein in budding yeast. Ski7 is a cofactor of the cytoplasmic exosome that functions in mRNA turnover and non-stop decay (NSD). The Ski7 II domain shares overall sequence similarity with the translational GTPase (trGTPase) Hbs1, but unlike other trGTPases, Ski7 might function as a GTP-binding protein rather than a GTP-hydrolyzing enzyme. The Ski7C is organized into three domains, with domain I adopting the alpha beta fold of GTP-binding domains, and domains II and III each adopting the structure of a closed beta barrel. Domains II and III appear to form a single unit and interact with the G domain, and the three domains interact intra-molecularly not only via their globular folds but also via extended segments.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Superkiller protein 7	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding protein-containing complex binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding protein-containing complex binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-macromolecule adaptor activity molecular adaptor activity pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation nuclear-transcribed mRNA catabolic process, non-stop decay regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process nonfunctional rRNA decay rRNA catabolic process rRNA metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process protein catabolic process protein metabolic process organonitrogen compound biosynthetic process translation nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay sulfur compound metabolic process translational elongation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.