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	PF02580	e1j7gA1	A: a/b three-layered sandwiches	X: DTD-like	H: DTD-like (Pfam 02580) (From Topology)	T: DTD-like (Pfam 02580)	F: PF02580	ECOD (1.6)

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	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 Ser(Gly)-tRNA(Ala) hydrolase activity D-tyrosyl-tRNA(Tyr) deacylase activity D-aminoacyl-tRNA deacylase activity RNA binding 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 Ser(Gly)-tRNA(Ala) hydrolase activity D-tyrosyl-tRNA(Tyr) deacylase activity D-aminoacyl-tRNA deacylase activity RNA binding binding organic cyclic compound binding tRNA binding nucleic acid binding	catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process organic substance metabolic process carboxylic acid catabolic process D-amino acid metabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process organic substance metabolic process carboxylic acid catabolic process D-amino acid metabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process non-proteinogenic amino acid catabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process alpha-amino acid catabolic process metabolic process cellular process small molecule catabolic process D-amino acid catabolic process organic substance catabolic process tRNA metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process ncRNA metabolic process RNA metabolic process macromolecule metabolic process nucleic acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.