7KA0

Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and phenylalanine

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	Class II aaRS and biotin synthetases	8102152	3000058	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8102152	3000058	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	Phe_tRNA-synt_N	e7ka0A1	A: alpha bundles	X: Long alpha-hairpin	H: tRNA-binding arm (From Topology)	T: tRNA-binding arm	F: Phe_tRNA-synt_N	ECOD (1.6)
A	tRNA-synt_2d	e7ka0A2	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2d	ECOD (1.6)
D	Phe_tRNA-synt_N	e7ka0D2	A: alpha bundles	X: Long alpha-hairpin	H: tRNA-binding arm (From Topology)	T: tRNA-binding arm	F: Phe_tRNA-synt_N	ECOD (1.6)
D	tRNA-synt_2d	e7ka0D1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2d	ECOD (1.6)
B	tRNA_bind_1	e7ka0B5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_bind_1	ECOD (1.6)
B	B3_4	e7ka0B6	A: beta complex topology	X: PheT/TilS domain (From Topology)	H: PheT/TilS domain (From Topology)	T: PheT/TilS domain	F: B3_4	ECOD (1.6)
B	B5	e7ka0B2	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: B5	ECOD (1.6)
B	pheT	e7ka0B3	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: pheT	ECOD (1.6)
B	FDX-ACB	e7ka0B4	A: a+b two layers	X: Alpha-beta plaits	H: Anticodon-binding domain of PheRS (From Topology)	T: Anticodon-binding domain of PheRS	F: FDX-ACB	ECOD (1.6)
B	tRNA-synt_2d_1	e7ka0B1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2d_1	ECOD (1.6)
E	tRNA_bind_1	e7ka0E5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_bind_1	ECOD (1.6)
E	B3_4	e7ka0E4	A: beta complex topology	X: PheT/TilS domain (From Topology)	H: PheT/TilS domain (From Topology)	T: PheT/TilS domain	F: B3_4	ECOD (1.6)
E	B5	e7ka0E6	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: B5	ECOD (1.6)
E	pheT	e7ka0E3	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: pheT	ECOD (1.6)
E	FDX-ACB	e7ka0E2	A: a+b two layers	X: Alpha-beta plaits	H: Anticodon-binding domain of PheRS (From Topology)	T: Anticodon-binding domain of PheRS	F: FDX-ACB	ECOD (1.6)
E	tRNA-synt_2d_1	e7ka0E1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2d_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF02912	Aminoacyl tRNA synthetase class II, N-terminal domain (Phe_tRNA-synt_N)	Aminoacyl tRNA synthetase class II, N-terminal domain	-	Domain
A, D	PF01409	tRNA synthetases class II core domain (F) (tRNA-synt_2d)	tRNA synthetases class II core domain (F)	Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain.	Domain
B, E	PF03483	B3/4 domain (B3_4)	B3/4 domain	This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins.	Domain
B, E	PF03484	tRNA synthetase B5 domain (B5)	tRNA synthetase B5 domain	This domain is found in phenylalanine-tRNA synthetase beta subunits.	Domain
B, E	PF03147	Ferredoxin-fold anticodon binding domain (FDX-ACB)	Ferredoxin-fold anticodon binding domain	This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold [1,2].	Domain
B, E	PF17759	Phenylalanyl tRNA synthetase beta chain CLM domain (tRNA_synthFbeta)	Phenylalanyl tRNA synthetase beta chain CLM domain	This domain corresponds to the catalytic like domain (CLM) in the beta chain of phe tRNA synthetase [1].	Domain
B, E	PF01588	Putative tRNA binding domain (tRNA_bind)	Putative tRNA binding domain	This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [2], human tyrosyl-tRNA synthetase [1], and endothelial-monocyte activating polypept ...	This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [2], human tyrosyl-tRNA synthetase [1], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases [2]. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme [2]. This domain may perform a common function in tRNA aminoacylation [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Phenylalanine--tRNA ligase alpha subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid phenylalanine-tRNA ligase activity catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding tRNA binding nucleic acid 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 organonitrogen compound metabolic process cellular metabolic process primary metabolic process translation 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 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 phenylalanyl-tRNA aminoacylation	cell periphery plasma membrane membrane cellular anatomical entity intracellular anatomical structure cytoplasm
B, E	Phenylalanine--tRNA ligase beta subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid phenylalanine-tRNA ligase activity catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding tRNA binding nucleic acid 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 organonitrogen compound metabolic process cellular metabolic process primary metabolic process translation 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 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 phenylalanyl-tRNA aminoacylation	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex intracellular anatomical structure catalytic complex cytoplasm phenylalanine-tRNA ligase complex external encapsulating structure cell wall peptidoglycan-based cell wall
C, F	tRNA(Phe)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, D	IPR002319	Phenylalanyl-tRNA synthetase	Domain
A, D	IPR004188	Phenylalanine-tRNA ligase, class II, N-terminal	Domain
A, D	IPR004529	Phenylalanyl-tRNA synthetase, class IIc, alpha subunit	Family
A, D	IPR022911	Phenylalanine-tRNA ligase alpha chain 1, bacterial	Family
A, D	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A, D	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
B, E	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily
B, E	IPR045060	Phenylalanine-tRNA ligase, class IIc, beta subunit	Family
B, E	IPR020825	Phenylalanyl-tRNA synthetase-like, B3/B4	Homologous Superfamily
B, E	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
B, E	IPR002547	tRNA-binding domain	Domain
B, E	IPR005147	tRNA synthetase, B5-domain	Domain
B, E	IPR005146	B3/B4 tRNA-binding domain	Domain
B, E	IPR041616	Phenylalanyl tRNA synthetase beta chain, core domain	Domain
B, E	IPR033714	Phenylalanly tRNA synthetase, tRNA-binding-domain	Domain
B, E	IPR005121	Ferrodoxin-fold anticodon-binding domain	Domain
B, E	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B, E	IPR036690	Ferrodoxin-fold anticodon-binding domain superfamily	Homologous Superfamily
B, E	IPR004532	Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type	Family