3M6V | pdb_00003m6v

Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P2 in complex with S-Adenosyl-L-Methionine

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)
A	EUF07530	e3m6vA5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: EUF07530	ECOD (1.6)
A	Methyltr_RsmB-F_1	e3m6vA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)
B	EUF07530	e3m6vB5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: EUF07530	ECOD (1.6)
B	Methyltr_RsmB-F_1	e3m6vB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltr_RsmB-F_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.1170	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Sun protein	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	2.30.130.60	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)
B	3.30.70.1170	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Sun protein	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	2.30.130.60	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17126	RsmF rRNA methyltransferase first C-terminal domain (RsmF_methylt_CI)	RsmF rRNA methyltransferase first C-terminal domain	This is the first of two distinct C-terminal domains of the 16S rRNA methyltransferase RsmF. It is necessary for stabilising the catalytic core, Pfam:PF01189.	Domain
A, B	PF17125	N-terminal domain of 16S rRNA methyltransferase RsmF (Methyltr_RsmF_N)	N-terminal domain of 16S rRNA methyltransferase RsmF	This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising t ...	This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising the catalytic core of the enzyme [1]. It has a ferredoxin-like fold.	Domain
A, B	PF01189	16S rRNA methyltransferase RsmB/F (Methyltr_RsmB-F)	16S rRNA methyltransferase RsmB/F	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) posi ...	This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	rRNA methylase	RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA binding binding nucleic acid binding	RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process RNA modification methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation ribonucleoprotein complex biogenesis rRNA processing RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process RNA modification methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation ribonucleoprotein complex biogenesis rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR031341	Ribosomal RNA small subunit methyltransferase F, N-terminal	Domain
A, B	IPR001678	SAM-dependent methyltransferase RsmB-F/NOP2-type domain	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR049560	SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic core	Domain
A, B	IPR023267	RNA (C5-cytosine) methyltransferase	Family
A, B	IPR031340	Ribosomal RNA small subunit methyltransferase F, first C-terminal domain	Domain
A, B	IPR048151	Ribosomal RNA small subunit methyltransferase F	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.