1QU3

INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH TRNA(ILE) AND MUPIROCIN

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d1qu3a1	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	Isoleucyl-tRNA synthetase (IleRS)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B [auth A]	d1qu3a2	All beta proteins	ValRS/IleRS/LeuRS editing domain	ValRS/IleRS/LeuRS editing domain	ValRS/IleRS/LeuRS editing domain	Isoleucyl-tRNA synthetase (IleRS)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B [auth A]	d1qu3a3	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Isoleucyl-tRNA synthetase (IleRS)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	Nucleotidylyl transferase	8044204	3001541	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	ValRS/IleRS/LeuRS editing domain	8042502	3001115	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Nucleotidylyl transferase	8044204	3001541	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8037147	3001786	SCOP2B (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]	tRNA-synt_1_2nd	e1qu3A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2nd	ECOD (1.6)
B [auth A]	Anticodon_1,tRNA-synt_1_1st	e1qu3A7	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: Anticodon_1,tRNA-synt_1_1st	ECOD (1.6)
B [auth A]	ileS_2nd	e1qu3A1	A: a+b three layers	X: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	H: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases (From Topology)	T: A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: ileS_2nd	ECOD (1.6)
B [auth A]	tRNA-synt_1_1st	e1qu3A2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1_1st	ECOD (1.6)
B [auth A]	ileS_1st_1	e1qu3A6	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: ileS_1st_1	ECOD (1.6)
B [auth A]	tRNA-synt_1_3rd	e1qu3A5	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: tRNA-synt_1_3rd	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]	3.90.740.10	Alpha Beta	Alpha-Beta Complex	Isoleucyl-tRNA Synthetase	domain 2	CATH (4.3.0)
B [auth A]	1.10.10.830	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ile-tRNA synthetase CP2 domain-like	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]	3.30.2320.20	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	Class I aminoacyl-tRNA synthetases (RS)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF08264	Anticodon-binding domain of tRNA ligase (Anticodon_1)	Anticodon-binding domain of tRNA ligase	This domain is found mainly hydrophobic tRNA synthetases. The domain binds to the anticodon of the tRNA ligase.	Domain
B [auth A]	PF00133	tRNA synthetases class I (I, L, M and V) (tRNA-synt_1)	tRNA synthetases class I (I, L, M and V)	Other tRNA synthetase sub-families are too dissimilar to be included.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth T]	ISOLEUCYL-TRNA	-	-	-
B [auth A]	ISOLEUCYL-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 isoleucine-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 hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity aminoacyl-tRNA editing activity hydrolase activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding tRNA binding nucleic acid binding	isoleucyl-tRNA aminoacylation amino acid activation tRNA aminoacylation cellular biosynthetic process cellular metabolic process 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 isoleucyl-tRNA aminoacylation amino acid activation tRNA aminoacylation cellular biosynthetic process cellular metabolic process 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	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR002301	Isoleucine-tRNA ligase	Family
B [auth A]	IPR050081	Isoleucine--tRNA ligase	Family
B [auth A]	IPR023585	Isoleucine-tRNA ligase, type 1	Family
B [auth A]	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
B [auth A]	IPR033708	Isoleucyl tRNA synthetase type 1, anticodon-binding domain	Domain
B [auth A]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
B [auth A]	IPR010663	Zinc finger, FPG/IleRS-type	Domain
B [auth A]	IPR002300	Aminoacyl-tRNA synthetase, class Ia	Domain
B [auth A]	IPR009008	Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain	Homologous Superfamily
B [auth A]	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
B [auth A]	IPR013155	Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding	Domain

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.