3RF9 | pdb_00003rf9

X-ray structure of RlmN from Escherichia coli

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Radical_SAM	e3rf9B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Radical_SAM	ECOD (develop294)
B	4HBT_3	e3rf9B2	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: 4HBT_3	ECOD (develop294)
A	ChapFlgA	e3rf9A1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: ChapFlgA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.150.530	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	1.10.150.530	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	4.10.180.60	Few Secondary Structures	Irregular	Black beetle virus capsid protein		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
A, B	PF21016	Ribosomal RNA large subunit methyltransferase N-terminal domain (RlmN_N)	Ribosomal RNA large subunit methyltransferase N-terminal domain	This entry represents the N-terminal domain from the dual-specificity RNA methyltransferase RlmN.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ribosomal RNA large subunit methyltransferase N	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity C-methyltransferase activity tRNA (adenine) methyltransferase activity tRNA (adenine(37)-C2)-methyltransferase activity methyltransferase activity catalytic activity rRNA methyltransferase activity tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity C-methyltransferase activity tRNA (adenine) methyltransferase activity tRNA (adenine(37)-C2)-methyltransferase activity methyltransferase activity catalytic activity rRNA methyltransferase activity catalytic activity, acting on a rRNA rRNA (adenine(2503)-C2-)-methyltransferase activity rRNA (adenine) methyltransferase activity RNA binding binding rRNA binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding tRNA binding cation binding ion binding metal ion binding	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation ribonucleoprotein complex biogenesis rRNA methylation rRNA processing rRNA modification cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process rRNA base methylation response to stimulus response to chemical response to antibiotic	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007197	Radical SAM	Domain
A, B	IPR027492	Dual-specificity RNA methyltransferase RlmN	Family
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR058240	Radical SAM superfamily	Homologous Superfamily
A, B	IPR040072	Methyltransferase (Class A)	Family
A, B	IPR048641	Dual-specificity RNA methyltransferase RlmN, N-terminal domain	Domain
A, B	IPR004383	Ribosomal RNA large subunit methyltransferase RlmN/Cfr	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.