2BYT

Thermus thermophilus Leucyl-tRNA synthetase complexed with a tRNAleu transcript in the post-editing conformation

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8042404	3001786	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidylyl transferase	8042406	3001541	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ValRS/IleRS/LeuRS editing domain	8042405	3001115	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotidylyl transferase	8042406	3001541	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	8042404	3001786	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	ValRS/IleRS/LeuRS editing domain	8042405	3001115	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Nucleotidylyl transferase	8042406	3001541	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Nucleotidylyl transferase	8042406	3001541	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)
A	tRNA-synt_1_2	e2bytA7	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	e2bytA6	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	leuS_3rd	e2bytA1	A: a+b two layers	X: beta-Grasp	H: beta-grasp fold domain in leucine-tRNA ligase (From Topology)	T: beta-grasp fold domain in leucine-tRNA ligase	F: leuS_3rd	ECOD (1.6)
A	tRNA-synt_1_1st	e2bytA8	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	tRNA-synt_1_3rd	e2bytA3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: tRNA-synt_1_3rd	ECOD (1.6)
A	tRNA-synt_1g	e2bytA5	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: tRNA-synt_1g	ECOD (1.6)
A	UNK_F_TYPE	e2bytA4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) (From Topology)	T: Rubredoxin-like domain in leucyl-tRNA synthetase (LS1)	F: UNK_F_TYPE	ECOD (1.6)
C [auth D]	tRNA-synt_1_2	e2bytD7	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: tRNA-synt_1_2	ECOD (1.6)
C [auth D]	Anticodon_1,tRNA-synt_1g	e2bytD8	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)
C [auth D]	leuS_3rd	e2bytD4	A: a+b two layers	X: beta-Grasp	H: beta-grasp fold domain in leucine-tRNA ligase (From Topology)	T: beta-grasp fold domain in leucine-tRNA ligase	F: leuS_3rd	ECOD (1.6)
C [auth D]	tRNA-synt_1_1st	e2bytD9	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)
C [auth D]	tRNA-synt_1_3rd	e2bytD5	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: tRNA-synt_1_3rd	ECOD (1.6)
C [auth D]	tRNA-synt_1g	e2bytD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: tRNA-synt_1g	ECOD (1.6)
C [auth D]	UNK_F_TYPE	e2bytD6	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) (From Topology)	T: Rubredoxin-like domain in leucyl-tRNA synthetase (LS1)	F: UNK_F_TYPE	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	2.30.210.10	Mainly Beta	Roll	Leucyl-tRNA synthetase, domain 3	Leucyl-tRNA synthetase, domain 3	CATH (4.3.0)
A	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)
A	3.10.20.590	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C [auth D]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C [auth D]	3.90.740.10	Alpha Beta	Alpha-Beta Complex	Isoleucyl-tRNA Synthetase	domain 2	CATH (4.3.0)
C [auth D]	2.30.210.10	Mainly Beta	Roll	Leucyl-tRNA synthetase, domain 3	Leucyl-tRNA synthetase, domain 3	CATH (4.3.0)
C [auth D]	1.10.730.10	Mainly Alpha	Orthogonal Bundle	Isoleucyl-tRNA Synthetase	Domain 1	CATH (4.3.0)
C [auth D]	3.10.20.590	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D]	PF13603	Leucyl-tRNA synthetase, editing domain (tRNA-synt_1_2)	Leucyl-tRNA synthetase, editing domain	This entry represents the editing domain in Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.	Domain
A, C [auth D]	PF09334	tRNA synthetases class I (M) (tRNA-synt_1g)	tRNA synthetases class I (M)	-	Family
A, C [auth D]	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, C [auth D]	PF14795	Leucine-tRNA synthetase-specific domain (Leucyl-specific)	Leucine-tRNA synthetase-specific domain	This short region is found only in leucyl-tRNA synthetases. It is flexibly linked to the enzyme-core by beta-ribbons structures [1]	Domain
A, C [auth D]	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, C [auth D]	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 cation binding metal ion binding	amino acid activation tRNA aminoacylation cellular biosynthetic process organonitrogen compound biosynthetic process RNA metabolic process amino acid metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process leucyl-tRNA aminoacylation 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 nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process protein metabolic process leucyl-tRNA aminoacylation 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	intracellular anatomical structure cytoplasm cellular anatomical entity
B, D [auth E]	TRNALEU TRANSCRIPT WITH ANTICODON CAG	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D]	IPR023356	Leucyl-tRNA synthetase, domain 3	Domain
A, C [auth D]	IPR025709	Leucyl-tRNA synthetase, editing domain	Domain
A, C [auth D]	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A, C [auth D]	IPR015413	Methionyl/Leucyl tRNA synthetase	Domain
A, C [auth D]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, C [auth D]	IPR002300	Aminoacyl-tRNA synthetase, class Ia	Domain
A, C [auth D]	IPR009008	Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain	Homologous Superfamily
A, C [auth D]	IPR009080	Aminoacyl-tRNA synthetase, class Ia, anticodon-binding	Homologous Superfamily
A, C [auth D]	IPR013155	Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding	Domain
A, C [auth D]	IPR002302	Leucine-tRNA ligase	Family

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.