3KNF

Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum

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)
C	d3knfc_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
D	d3knfd_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
E	d3knfe_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
A	d3knfa_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d3knfb_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
F	d3knff_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DTD-like	8074792	3000522	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)
C	Tyr_Deacylase	e3knfC1	A: a/b three-layered sandwiches	X: DTD-like	H: DTD-like (Pfam 02580) (From Topology)	T: DTD-like (Pfam 02580)	F: Tyr_Deacylase	ECOD (1.6)
D	Tyr_Deacylase	e3knfD1	A: a/b three-layered sandwiches	X: DTD-like	H: DTD-like (Pfam 02580) (From Topology)	T: DTD-like (Pfam 02580)	F: Tyr_Deacylase	ECOD (1.6)
E	Tyr_Deacylase	e3knfE1	A: a/b three-layered sandwiches	X: DTD-like	H: DTD-like (Pfam 02580) (From Topology)	T: DTD-like (Pfam 02580)	F: Tyr_Deacylase	ECOD (1.6)
A	Tyr_Deacylase	e3knfA1	A: a/b three-layered sandwiches	X: DTD-like	H: DTD-like (Pfam 02580) (From Topology)	T: DTD-like (Pfam 02580)	F: Tyr_Deacylase	ECOD (1.6)
B	Tyr_Deacylase	e3knfB1	A: a/b three-layered sandwiches	X: DTD-like	H: DTD-like (Pfam 02580) (From Topology)	T: DTD-like (Pfam 02580)	F: Tyr_Deacylase	ECOD (1.6)
F	Tyr_Deacylase	e3knfF1	A: a/b three-layered sandwiches	X: DTD-like	H: DTD-like (Pfam 02580) (From Topology)	T: DTD-like (Pfam 02580)	F: Tyr_Deacylase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
D	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
E	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
A	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
B	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
F	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02580	D-Tyr-tRNA(Tyr) deacylase (Tyr_Deacylase)	D-Tyr-tRNA(Tyr) deacylase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	D-tyrosyl-tRNA(Tyr) deacylase	hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity aminoacyl-tRNA editing activity hydrolase activity catalytic activity, acting on a tRNA Gly-tRNA(Ala) hydrolase activity catalytic activity D-aminoacyl-tRNA deacylase activity deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity binding nucleoside phosphate binding hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity aminoacyl-tRNA editing activity hydrolase activity catalytic activity, acting on a tRNA Gly-tRNA(Ala) hydrolase activity catalytic activity D-aminoacyl-tRNA deacylase activity deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding RNA binding tRNA binding nucleic acid binding	tRNA metabolic process nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process nucleic acid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR003732	D-aminoacyl-tRNA deacylase DTD	Family
A, B, C, D, E A, B, C, D, E, F	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily	Homologous Superfamily

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.