5XJ2 | pdb_00005xj2

Structure of spRlmCD with U747 RNA

External Resource: Annotation

Domain Annotation: ECOD Classification
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	TRAM	e5xj2A2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: TRAM	ECOD (1.6)
A	Methyltransf_11_2	e5xj2A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
B	TRAM	e5xj2B2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: TRAM	ECOD (1.6)
B	Methyltransf_11_2	e5xj2B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
C	TRAM	e5xj2C1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: TRAM	ECOD (1.6)
C	Methyltransf_11_2	e5xj2C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
D	TRAM	e5xj2D2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: TRAM	ECOD (1.6)
D	Methyltransf_11_2	e5xj2D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05958	tRNA (Uracil-5-)-methyltransferase (tRNA_U5-meth_tr)	tRNA (Uracil-5-)-methyltransferase	-	Family
A, B, C, D	PF01938	TRAM domain (TRAM)	TRAM domain	This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Uncharacterized RNA methyltransferase SP_1029	RNA 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 C-methyltransferase activity rRNA (uridine-C5-)-methyltransferase activity rRNA (uridine) methyltransferase activity methyltransferase activity catalytic activity	ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing 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 primary metabolic process ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing 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 primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process rRNA base methylation RNA methylation	-
E [auth G]	RNA (5'-R(GPGPCPAPCPGPUPGPCPU)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002792	TRAM domain	Domain
A, B, C, D	IPR010280	(Uracil-5)-methyltransferase family	Family
A, B, C, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D	IPR030391	RNA methyltransferase TrmA, conserved site	Conserved Site
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B, C, D	IPR030390	RNA methyltransferase TrmA, active site	Active Site

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.