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	Tyr_Deacylase	e1j7gA1	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)
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-aminoacyl-tRNA deacylase activity deacylase activity D-tyrosyl-tRNA(Tyr) deacylase activity RNA 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-aminoacyl-tRNA deacylase activity 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 organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process D-amino acid metabolic process catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process alpha-amino acid catabolic 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

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.