4ZU9

Crystal structure of bacterial selenocysteine-specific elongation factor EF-Sec

External Resource: Annotation

Domain Annotation: ECOD Classification
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	PF03144	e4zu9A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PF03144	ECOD (1.6)
A	F_UNCLASSIFIED	e4zu9A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF09107	e4zu9A7	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF09107	ECOD (1.6)
A	PF21580	e4zu9A6	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF21580	ECOD (1.6)
A	PF22153	e4zu9A4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF22153	ECOD (1.6)
A	PF22154	e4zu9A5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF22154	ECOD (1.6)
A	PF00009	e4zu9A1	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)

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	PF21580	Elongation factor SelB, third winged-helix domain (SelB_WHD3)	Elongation factor SelB, third winged-helix domain	This domain is found in Elongation factor SelB from Aquifex aeolicus and similar bacterial proteins. SelB is a selenocysteine(Sec)-specific elongation factor that brings the selenocysteinyl-tRNA(Sec) to the ribosome. It consists of three EF-Tu-like d ...	This domain is found in Elongation factor SelB from Aquifex aeolicus and similar bacterial proteins. SelB is a selenocysteine(Sec)-specific elongation factor that brings the selenocysteinyl-tRNA(Sec) to the ribosome. It consists of three EF-Tu-like domains (D1-3, where Pfam:PF00009 is the first one), followed by four winged-helix domains (WHD1-4). This entry represents the third winged-helix domains (WHD3) [1].	Domain
A	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
A	PF09107	Elongation factor SelB, winged helix (SelB-wing_3)	Elongation factor SelB, winged helix	Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DN ...	Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Elongation factor SelB	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 RNA 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 RNA 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 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	selenocysteine incorporation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process selenocysteine incorporation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process translational readthrough gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A	IPR048638	Elongation factor SelB-like, third winged-helix domain	Domain
A	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A	IPR015191	Elongation factor SelB, fourth winged-helix domain	Domain
A	IPR005225	Small GTP-binding protein domain	Domain
A	IPR004535	Translation elongation factor, selenocysteine-specific	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.