Annotations: 1J7G

Structure of YihZ from Haemophilus influenzae (HI0670), a D-Tyr-tRNA(Tyr) deacylase

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1j7ga_	Alpha and beta proteins (a/b)	DTD-like	DTD-like	DTD-like	D-Tyr tRNAtyr deacylase, DTD	(Haemophilus influenzae Rd KW20 ) [TaxId: 71421 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DTD-like	8019892	4003261	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DTD-like	8032272	3000522	SCOP2 (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	Glyco_hydro_20b	e1j7gA1	A: beta barrels	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	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 Ser(Gly)-tRNA(Ala) hydrolase 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 Ser(Gly)-tRNA(Ala) hydrolase activity D-aminoacyl-tRNA deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity RNA binding binding tRNA binding nucleic acid binding	catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process non-proteinogenic amino acid metabolic process carboxylic acid catabolic process D-amino acid metabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process D-amino acid catabolic process catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process non-proteinogenic amino acid metabolic process carboxylic acid catabolic process D-amino acid metabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process D-amino acid catabolic process amino acid catabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA 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	IPR003732	D-aminoacyl-tRNA deacylase DTD	Family
A	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	D-aminoacyl-tRNA deacylase M-CSA #748	YihZ, a D-Tyr-tRNA(Tyr) deacylase from Haemophilus influenzae is an 'editing enzyme'. It removes D-tyrosine and other D-amino acids from charged tRNAs, thereby preventing incorrect incorporation of D-amino acids in proteins. This is important, as the presence of D-amino acids can impair correct folding of proteins. Any incorrectly charged tRNA must be removed, and YihZ catalyses the hydrolysis of the ester link between D-Tyr and tRNA. This enzyme exhibits broad specificity towards D-amino acids, but it is inactive toward L-aminoacylated tRNAs and N-blocked D-aminoacylated tRNAs.	Defined by 3 residues: GLN:A-78PHE:A-79THR:A-80 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1 (PDB Primary Data) Search M-CSA Motif + EC 3.1 EC: 3.1.1.96 (UniProt) Search M-CSA Motif + EC 3.1.1.96

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