1F7U

CRYSTAL STRUCTURE OF THE ARGINYL-TRNA SYNTHETASE COMPLEXED WITH THE TRNA(ARG) AND L-ARG

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)
B [auth A]	d1f7ua1	All alpha proteins	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Arginyl-tRNA synthetase (ArgRS)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B [auth A]	d1f7ua2	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Arginyl-tRNA synthetase (ArgRS)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B [auth A]	d1f7ua3	Alpha and beta proteins (a+b)	RRF/tRNA synthetase additional domain-like	Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain	Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain	Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	Arginyl-tRNA synthetase (ArgRS) N-terminal 'additional' domain	8020574	4001410	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Family	Class I aminoacyl-tRNA synthetases (RS) catalytic domain	8020573	4003807	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Family	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8020571	4000856	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Arginyl-tRNA synthetase (ArgRS) N-terminal 'additional' domain	8032954	3001515	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Nucleotidylyl transferase	8032953	3001541	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8032951	3001786	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)
B [auth A]	DALR_1,tRNA-synt_1d	e1f7uA1	A: alpha bundles	X: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: DALR_1,tRNA-synt_1d	ECOD (1.6)
B [auth A]	Arg_tRNA_synt_N	e1f7uA2	A: a+b two layers	X: RRF/tRNA synthetase additional domain-like	H: Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain (From Topology)	T: Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain	F: Arg_tRNA_synt_N	ECOD (1.6)
B [auth A]	tRNA-synt_1d	e1f7uA3	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1d	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B [auth A]	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)
B [auth A]	3.30.1360.70	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF03485	Arginyl tRNA synthetase N terminal domain (Arg_tRNA_synt_N)	Arginyl tRNA synthetase N terminal domain	This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition [1].	Domain
B [auth A]	PF00750	tRNA synthetases class I (R) (tRNA-synt_1d)	tRNA synthetases class I (R)	-	Family
B [auth A]	PF05746	DALR anticodon binding domain (DALR_1)	DALR anticodon binding domain	This all alpha helical domain is the anticodon binding domain in Arginyl and glycyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	TRNA(ARG)	-	-	-
B [auth A]	ARGINYL-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 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 arginine-tRNA ligase activity catalytic activity ligase activity	amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process arginyl-tRNA aminoacylation nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process arginyl-tRNA aminoacylation nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process organonitrogen compound metabolic process cellular metabolic process primary metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process mitochondrial translation mitochondrial gene expression	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR036695	Arginyl tRNA synthetase N-terminal domain superfamily	Homologous Superfamily
B [auth A]	IPR005148	Arginyl tRNA synthetase N-terminal domain	Domain
B [auth A]	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
B [auth A]	IPR001278	Arginine-tRNA ligase	Family
B [auth A]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
B [auth A]	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
B [auth A]	IPR035684	Arginyl-tRNA synthetase, catalytic core domain	Domain
B [auth A]	IPR008909	DALR anticodon binding	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
B [auth A]	arginine-tRNA ligase M-CSA #235	Arginyl-tRNA synthetase (ArgRS), isolated from Saccharomyces cerevisiae, catalyses the esterification of arginine to the 3'-terminal adenosine of a tRNA molecule. The reaction proceeds via an aminoacyl-adenylate intermediate and is ATP dependent. Although the tRNA molecule is not directly involved in the formation of the arginyl-adenylate intermediate, the tRNA must be bound to the enzyme before the reaction can occur. This may be due to conformational changes induced in the enzyme upon binding tRNA, as suggested for other aminoacyl-tRNA synthetases. ArgRS is a class 1a aminoacyl-tRNA synthease based on its structure, or class 1C when considering its requirement of tRNA.	Defined by 3 residues: LYS:B-156 [auth A-156]HIS:B-159 [auth A-159]HIS:B-162 [auth A-162] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.1.1.19 (PDB Primary Data) Search M-CSA Motif + EC 6.1.1.19

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.