1YI8 | pdb_00001yi8

Crystal structure of tryptophanyl trRNA synthetase II from Deinococcus radiodurans in complex with L-Trp

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C	d1yi8c_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
B [auth A]	d1yi8a_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)
A [auth B]	d1yi8b_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Nucleotidylyl transferase	automated matches	automated matches	(Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 ) [TaxId: 243230 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Nucleotidylyl transferase	8070103	3001541	SCOP2B (2022-06-29)
B [auth A]	SCOP2 Family	Class I aminoacyl-tRNA synthetases (RS), catalytic domain	8070102	4003807	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Nucleotidylyl transferase	8070103	3001541	SCOP2 (2022-06-29)
A [auth B]	SCOP2B Superfamily	Nucleotidylyl transferase	8070103	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)
C	Sigma_1_2	e1yi8C1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (develop294)
B [auth A]	Sigma_1_2	e1yi8A1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (develop294)
A [auth B]	Toxin_cobra-type	e1yi8B1	A: alpha bundles	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: Toxin_cobra-type	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A], C	tryptophanyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 catalytic activity, acting on RNA tryptophan-tRNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity	amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process tryptophanyl-tRNA aminoacylation biosynthetic process amino acid activation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation protein biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process tryptophanyl-tRNA aminoacylation biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C	IPR050203	Tryptophan--tRNA ligase	Family
A [auth B], B [auth A], C	IPR002305	Aminoacyl-tRNA synthetase, class Ic	Family
A [auth B], B [auth A], C	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site	Conserved Site
A [auth B], B [auth A], C	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A [auth B], B [auth A], C	IPR002306	Tryptophan-tRNA ligase	Family

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.