3RFA

X-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation
Structure Motif: Primary M-CSA Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PF21016	e3rfaB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF21016	ECOD (1.6)
B	PF04055	e3rfaB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055	ECOD (1.6)
A	PF21016	e3rfaA3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF21016	ECOD (1.6)
A	PF04055	e3rfaA4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF04055	ECOD (1.6)

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)

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 organic cyclic compound 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	cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation cellular biosynthetic process RNA metabolic process nucleobase-containing compound metabolic process organic substance metabolic process tRNA processing organic substance biosynthetic process RNA processing cellular metabolic process tRNA modification primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process methylation macromolecule modification ncRNA metabolic process nucleic acid catabolic process 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	intracellular anatomical structure cytoplasm cellular anatomical entity 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	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	SMC	Parent Component: CYS RESID: AA0234 PSI-MOD : S-methyl-L-cysteine MOD:00239

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	adenosine C2 methyltransferase (RlmN) M-CSA #938	23S rRNA (adenine(2503)-C(2))-methyltransferase (RlmN) specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase centre and thus would serve to optimise ribosomal fidelity. Unmodified tRNA is not a suitable substrate for RlmN, which suggests that RlmN works in a late step during tRNA maturation. RlmN is a member of the Radical SAM superfamily.	Defined by 6 residues: GLU:B-105CYS:B-118CYS:B-125CYS:B-129CYS:B-132CYS:B-355 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.192 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.192

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 R01GM133198.