2B3J | pdb_00002b3j

Crystal Structure of Staphylococcus aureus tRNA Adenosine Deaminase, TadA, in Complex with RNA

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)
H [auth D]	d2b3jd_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	tRNA adenosine deaminase TadA	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
G [auth C]	d2b3jc_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	tRNA adenosine deaminase TadA	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
F [auth B]	d2b3jb_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	tRNA adenosine deaminase TadA	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
E [auth A]	d2b3ja1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Deoxycytidylate deaminase-like	tRNA adenosine deaminase TadA	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth D]	SCOP2B Superfamily	Cytidine deaminase-like	8037592	3001838	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Cytidine deaminase-like	8037592	3001838	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Cytidine deaminase-like	8037592	3001838	SCOP2B (2022-06-29)
E [auth A]	SCOP2 Family	Deoxycytidylate deaminase-like	8025213	4000564	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	Cytidine deaminase-like	8037592	3001838	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)
H [auth D]	dCMP_cyt_deam_1	e2b3jD1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
G [auth C]	dCMP_cyt_deam_1	e2b3jC1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
F [auth B]	dCMP_cyt_deam_1	e2b3jB1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
E [auth A]	dCMP_cyt_deam_1	e2b3jA1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth D]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
G [auth C]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
F [auth B]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
E [auth A]	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth F], C [auth G], D [auth H]	anticodon stem-loop of t-RNA-Arg2 (nucleotides 27-42)	-	-	-
E [auth A], F [auth B], G [auth C], H [auth D]	tRNA adenosine deaminase	catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity, acting on a tRNA deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines adenosine deaminase activity tRNA-specific adenosine deaminase activity catalytic activity tRNA-specific adenosine-34 deaminase activity cation binding transition metal ion binding zinc ion binding catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity, acting on a tRNA deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines adenosine deaminase activity tRNA-specific adenosine deaminase activity catalytic activity tRNA-specific adenosine-34 deaminase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process adenosine to inosine editing tRNA processing tRNA wobble base modification RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process adenosine to inosine editing tRNA processing tRNA wobble base modification RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification tRNA wobble adenosine to inosine editing base conversion or substitution editing biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B], G [auth C], H [auth D]	IPR058535	MafB19-deam	Unknown
E [auth A], F [auth B], G [auth C], H [auth D]	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
E [auth A], F [auth B], G [auth C], H [auth D]	IPR028883	tRNA-specific adenosine deaminase	Family
E [auth A], F [auth B], G [auth C], H [auth D]	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
E [auth A], F [auth B], G [auth C], H [auth D]	IPR016193	Cytidine deaminase-like	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.