Annotations: 5XAQ

Crystal structure of Animalia-specific tRNA deacylase from Mus musculus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	d5xaqb_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5xaqa_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	DTD-like	8083643	4003261	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DTD-like	8083644	3000522	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	DTD-like	8083644	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)
B	OB_NTP_bind	e5xaqB1	A: beta barrels	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: OB_NTP_bind	ECOD (v294.2)
A	Ribosomal_S13	e5xaqA1	A: beta barrels	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C	T: FAD-linked reductases-C	F: Ribosomal_S13	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Probable D-tyrosyl-tRNA(Tyr) deacylase 2	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 Ala-tRNA(Thr) deacylase activity D-aminoacyl-tRNA deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity RNA 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 Ala-tRNA(Thr) deacylase activity D-aminoacyl-tRNA deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity RNA binding 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 biological regulation aminoacyl-tRNA metabolism involved in translational fidelity regulation of biological quality regulation of translational fidelity	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003732	D-aminoacyl-tRNA deacylase DTD	Family
A, B	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.