1WKB

Crystal Structure of Leucyl-tRNA Synthetase from the Archaeon Pyrococcus horikoshii Reveals a Novel Editing Domain Orientation

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	tRNA-synt_1_2	e1wkbA5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (1.6)
A	Anticodon_1,tRNA-synt_1g	e1wkbA4	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_1g	ECOD (1.6)
A	tRNA-synt_1_1st	e1wkbA2	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)
A	leuS_1st	e1wkbA3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: leuS_1st	ECOD (1.6)
A	leuS_2nd	e1wkbA1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: leuS_2nd	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	3.90.740.10	Alpha Beta	Alpha-Beta Complex	Isoleucyl-tRNA Synthetase	domain 2	CATH (4.3.0)
A	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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	Leucyl-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 leucine-tRNA ligase activity 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	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 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 leucyl-tRNA aminoacylation	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020791	Leucine-tRNA ligase, archaeal	Family
A	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR002300	Aminoacyl-tRNA synthetase, class Ia	Domain
A	IPR004493	Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic	Family
A	IPR009008	Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain	Homologous Superfamily
A	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
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.