5APG | pdb_00005apg

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from Vulcanisaeta distributa

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Tsr3-like	8045174	4004337	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta knot	8057033	3001122	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8057033	3001122	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	alpha/beta knot	8057033	3001122	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	Ribo_biogen_C	e5apgA1	A: a/b three-layered sandwiches	X: alpha/beta knot	H: alpha/beta knot	T: alpha/beta knot	F: Ribo_biogen_C	ECOD (v294.1)
B	VTC	e5apgB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: VTC	ECOD (v294.1)
C	VTC	e5apgC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: ARM repeat	T: ARM repeat	F: VTC	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF04034	Ribosome biogenesis protein, C-terminal (Ribo_biogen_C)	Ribosome biogenesis protein, C-terminal	This family represents the C-terminal domain of some putative ribosome biogenesis proteins in archaea. It has also been identified in the eukaryotic protein Tsr3, which is involved in ribosomal RNA biogenesis [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	TSR3	catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA catalytic activity transferase activity, transferring alkyl or aryl (other than methyl) groups rRNA small subunit aminocarboxypropyltransferase activity cation binding binding ion binding S-adenosyl-L-methionine binding sulfur compound binding small molecule binding	ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis rRNA pseudouridine synthesis primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR022968	16S/18S rRNA aminocarboxypropyltransferase Tsr3	Family
A, B, C	IPR007177	16S/18S rRNA aminocarboxypropyltransferase Tsr3, C-terminal	Domain

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.