2YXN

Structual basis of azido-tyrosine recognition by engineered bacterial Tyrosyl-tRNA synthetase

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)
A	d2yxna_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	Tyrosyl-tRNA synthetase (TyrRS)	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotidylyl transferase	8096790	3001541	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)
A	tRNA-synt_1b_1	e2yxnA1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: tRNA-synt_1b_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.10.240.10	Mainly Alpha	Orthogonal Bundle	Tyrosyl-Transfer RNA Synthetase	Tyrosyl-Transfer RNA Synthetase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00579	tRNA synthetases class I (W and Y) (tRNA-synt_1b)	tRNA synthetases class I (W and Y)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Tyrosyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity tyrosine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity RNA binding nucleic acid binding	tRNA metabolic process nucleobase-containing compound metabolic process amino acid activation tRNA aminoacylation RNA metabolic process metabolic process primary metabolic process amino acid metabolic process macromolecule metabolic process nucleic acid metabolic process tyrosyl-tRNA aminoacylation cellular biosynthetic process cellular metabolic process translation tRNA metabolic process nucleobase-containing compound metabolic process amino acid activation tRNA aminoacylation RNA metabolic process metabolic process primary metabolic process amino acid metabolic process macromolecule metabolic process nucleic acid metabolic process tyrosyl-tRNA aminoacylation cellular biosynthetic process cellular metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process biosynthetic process cellular process protein metabolic process	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002942	RNA-binding S4 domain	Domain
A	IPR024107	Tyrosine-tRNA ligase, bacterial-type, type 1	Family
A	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR002307	Tyrosine-tRNA ligase	Family
A	IPR002305	Aminoacyl-tRNA synthetase, class Ic	Family
A	IPR024088	Tyrosine-tRNA ligase, bacterial-type	Family
A	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily

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.