Annotations: 5J61

D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with glycyl-3'-aminoadenosine at 2.10 Angstrom resolution

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)
H	d5j61h_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
G	d5j61g_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
F	d5j61f_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
E	d5j61e_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
D	d5j61d_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
C	d5j61c_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
B	d5j61b_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	(Plasmodium falciparum 3D7 ) [TaxId: 36329 ],	SCOPe (2.08)
A	d5j61a_	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)
H	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DTD-like	8074792	3000522	SCOP2B (2022-06-29)
A	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)
H		e5j61H1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)
G		e5j61G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)
F		e5j61F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)
E		e5j61E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)
D		e5j61D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)
C		e5j61C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)
B		e5j61B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)
A		e5j61A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.50.80.10	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
G	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)
E	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)
C	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)
A	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, G, H	PF02580	D-Tyr-tRNA(Tyr) deacylase (Tyr_Deacylase)	D-Tyr-tRNA(Tyr) deacylase	This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tR ...	This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologues of the deacylase are found in many cells [1].The D-aminoacyl-tRNA deacylase (DTD) enzyme is homodimeric with two active sites located at the dimeric interface. Each active site carries an invariant Gly-cisPro dipeptide motif in each monomer. The interaction between the dipeptide motifs from each monomer ensures substrate stereospecificity. This family also includes a subclass of DTDs which is present in Chordata and harbors a Gly-transPro motif. The cis to trans switch is the key to Animal DTDs (ATD) gaining of L-chiral selectivity. This 'gain of function' through relaxation of substrate chiral specificity underlies ATD's capability of correcting the error in tRNA selection [2].	Domain

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, G, H	D-tyrosyl-tRNA(Tyr) deacylase	Gly-tRNA(Ala) deacylase activity aminoacyl-tRNA deacylase activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid deacylase activity carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA catalytic activity D-aminoacyl-tRNA deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity binding nucleoside phosphate binding Gly-tRNA(Ala) deacylase activity aminoacyl-tRNA deacylase activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid deacylase activity carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA catalytic activity D-aminoacyl-tRNA deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity binding nucleoside phosphate 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, G, H	IPR003732	D-aminoacyl-tRNA deacylase DTD	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily	Homologous Superfamily

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.