1J09

Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1j09a1	All alpha proteins	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	C-terminal domain of glutamyl-tRNA synthetase (GluRS)	C-terminal domain of glutamyl-tRNA synthetase (GluRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1j09a2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Glutamyl-tRNA synthetase (GluRS)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	C-terminal domain of glutamyl-tRNA synthetase (GluRS)	8030186	4001149	SCOP2 (2022-06-29)
A	SCOP2 Family	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	8030189	4003807	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	8042565	3000922	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotidylyl transferase	8042568	3001541	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	gltX_2	e1j09A1	A: alpha arrays	X: HTH	H: An anticodon-binding domain of class I aminoacyl-tRNA synthetases (From Topology)	T: An anticodon-binding domain of class I aminoacyl-tRNA synthetases	F: gltX_2	ECOD (1.6)
A	tRNA-synt_1c_1	e1j09A3	A: alpha bundles	X: Zn-binding domain in glutaminyl-tRNA synthetase (From Topology)	H: Zn-binding domain in glutaminyl-tRNA synthetase (From Topology)	T: Zn-binding domain in glutaminyl-tRNA synthetase	F: tRNA-synt_1c_1	ECOD (1.6)
A	tRNA-synt_1c_1	e1j09A2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1c_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.10.1160.10	Mainly Alpha	Orthogonal Bundle	Glutamyl-tRNA Synthetase	domain 2	CATH (4.3.0)
A	3.90.800.10	Alpha Beta	Alpha-Beta Complex	Glutamyl-tRNA Synthetase	domain 3	CATH (4.3.0)
A	1.10.8.70	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.10.10.350	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF19269	Anticodon binding domain (Anticodon_2)	Anticodon binding domain	This entry represents the anticodon binding domain found at the C-terminus of the class-I glutamyl tRNA synthetase enzyme.	Domain
A	PF00749	tRNA synthetases class I (E and Q), catalytic domain (tRNA-synt_1c)	tRNA synthetases class I (E and Q), catalytic domain	Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organisms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Glutamyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding glutamate-tRNA ligase activity ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding tRNA binding nucleic acid binding	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process glutamyl-tRNA aminoacylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020751	Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2	Homologous Superfamily
A	IPR000924	Glutamyl/glutaminyl-tRNA synthetase	Family
A	IPR033910	Glutamyl-tRNA synthetase	Domain
A	IPR020058	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain	Domain
A	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR045462	Aminoacyl-tRNA synthetase, class I, anticodon-binding	Domain
A	IPR049940	Glutamyl-Q tRNA(Asp) synthetase/Glutamate--tRNA ligase	Family
A	IPR004527	Glutamate-tRNA ligase, bacterial/mitochondrial	Family
A	IPR020752	Glutamate-tRNA synthetase, class I, anticodon-binding domain, subdomain 1	Homologous Superfamily
A	IPR008925	Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	glutamate-tRNA ligase M-CSA #318	Glutamyl tRNA synthase is able to catalyse the attachment of the amino acid glutamate to its corresponding tRNA molecule, utilising ATP in the process. It is a member of the class I tRNA synthases, and among this group is one of the three known to be unable to catalyse the activation of the amino acid by reaction with ATP unless the tRNA that the amino acid is subsequently transferred to is also present. The enzyme described here, from Thermus thermophilus, displays homology with the other class I tRNA synthases, such as Glutamine tRNA synthase, and is assumed to share a common evolutionary origin with these enzymes, as well as a conserved mechanism by which the reaction occurs.	Defined by 1 residue: LYS:A-246 \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 6.1.1.17 (PDB Primary Data)

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 R01GM157729.