4AUK | pdb_00004auk

Crystal structure of C2498 2'-O-ribose methyltransferase RlmM 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
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Elong_Iki1	e4aukB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Elong_Iki1	ECOD (v294.1)
B	UvrA_DNA-bind	e4aukB3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: UvrA_DNA-bind	ECOD (v294.1)
A	Elong_Iki1	e4aukA1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Elong_Iki1	ECOD (v294.1)
A	UvrA_DNA-bind	e4aukA3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: UvrA_DNA-bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.2810	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.2300.20	Alpha Beta	2-Layer Sandwich	THUMP fold		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)
A	3.30.70.2810	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.2300.20	Alpha Beta	2-Layer Sandwich	THUMP fold		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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18125	RlmM ferredoxin-like domain (RlmM_FDX)	RlmM ferredoxin-like domain	This domain is found in Ribosomal methyltransferase RlmM (YdgE) present in E. coli. RlmM catalyzes the S-adenosyl methionine (AdoMet)-dependent 2'O methylation of C2498 in 23S ribosomal RNA. The domain is ferredoxin-like and forms part of the THUMP d ...	This domain is found in Ribosomal methyltransferase RlmM (YdgE) present in E. coli. RlmM catalyzes the S-adenosyl methionine (AdoMet)-dependent 2'O methylation of C2498 in 23S ribosomal RNA. The domain is ferredoxin-like and forms part of the THUMP domain which binds RNA. THUMP domains typically have low sequence similarity [1].	Domain
A, B	PF01728	FtsJ-like methyltransferase (FtsJ)	FtsJ-like methyltransferase	-	Family
A, B	PF21239	Ribosomal RNA large subunit methyltransferase M, N-terminal (RLMM_N)	Ribosomal RNA large subunit methyltransferase M, N-terminal	This is the THUMP-like domain of Ribosomal RNA large subunit methyltransferase M (RLMM), adjacent the ferredoxin-like domain (Pfam:PF18125), which together constitutes the N-terminal domain [1]. RlmM specifically catalyses the 2'-O-methylation of nuc ...	This is the THUMP-like domain of Ribosomal RNA large subunit methyltransferase M (RLMM), adjacent the ferredoxin-like domain (Pfam:PF18125), which together constitutes the N-terminal domain [1]. RlmM specifically catalyses the 2'-O-methylation of nucleotide C2498 in the peptidyl transferase loop of 23S rRNA [1].	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 M	rRNA (cytosine-2'-O-ribose)-methyltransferase activity RNA methyltransferase activity O-methyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity catalytic activity rRNA (cytosine) methyltransferase activity RNA 2'-O-methyltransferase activity	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic 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	IPR040739	RlmM ferredoxin-like domain	Domain
A, B	IPR011224	Ribosomal RNA large subunit methyltransferase M	Family
A, B	IPR002877	Ribosomal RNA methyltransferase, FtsJ domain	Domain
A, B	IPR048646	Ribosomal RNA large subunit methyltransferase M, THUMP-like domain	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	CSS	Parent Component: CYS RESID: AA0269 PSI-MOD : L-cysteine persulfide MOD:00274

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.

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