2BH2

Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2bh2b1	All beta proteins	OB-fold	Nucleic acid-binding proteins	TRAM domain	rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2bh2b2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	(Uracil-5-)-methyltransferase	rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2bh2a1	All beta proteins	OB-fold	Nucleic acid-binding proteins	TRAM domain	rRNA (Uracil-5-)-methyltransferase RumA, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2bh2a2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	(Uracil-5-)-methyltransferase	rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8035254	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8035253	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8035254	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8035253	3000135	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PF01938	e2bh2B1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01938	ECOD (1.6)
B	F_UNCLASSIFIED	e2bh2B3	A: a+b two layers	X: RumA insert domain (From Topology)	H: RumA insert domain (From Topology)	T: RumA insert domain	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF05958	e2bh2B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF05958	ECOD (1.6)
A	PF01938	e2bh2A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF01938	ECOD (1.6)
A	PF05958	e2bh2A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF05958	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	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	2.40.50.1070	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	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	2.40.50.1070	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05958	tRNA (Uracil-5-)-methyltransferase (tRNA_U5-meth_tr)	tRNA (Uracil-5-)-methyltransferase	-	Family
A, B	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	23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA	RNA binding binding organic cyclic compound binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding 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 RNA binding binding organic cyclic compound binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding 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 cation binding transition metal ion binding iron ion binding ion binding metal ion binding	ribonucleoprotein complex biogenesis cellular biosynthetic process rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process ribonucleoprotein complex biogenesis cellular biosynthetic process rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation 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 rRNA base methylation RNA methylation	-
C, D	23S RIBOSOMAL RNA 1932-1968	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002792	TRAM domain	Domain
A, B	IPR010280	(Uracil-5)-methyltransferase family	Family
A, B	IPR001566	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR030391	RNA methyltransferase TrmA, conserved site	Conserved Site
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR030390	RNA methyltransferase TrmA, active site	Active Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.