5TWJ

Crystal Structure of RlmH in Complex with S-Adenosylmethionine

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)
A [auth C]	d5twjc1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A [auth C]	d5twjc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth D]	d5twjd1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth D]	d5twjd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d5twja1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d5twja2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d5twjb1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d5twjb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A [auth C]	SCOP2B Superfamily	alpha/beta knot	8043915	3001122	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	alpha/beta knot	8043915	3001122	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	alpha/beta knot	8043915	3001122	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	alpha/beta knot	8043915	3001122	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)
A [auth C]	SPOUT_MTase	e5twjC1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SPOUT_MTase	ECOD (1.6)
B [auth D]	SPOUT_MTase	e5twjD1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SPOUT_MTase	ECOD (1.6)
C [auth A]	SPOUT_MTase	e5twjA1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SPOUT_MTase	ECOD (1.6)
D [auth B]	SPOUT_MTase	e5twjB1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: SPOUT_MTase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth C]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
B [auth D]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
C [auth A]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
D [auth B]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth D], C [auth A], D [auth B]	PF02590	Predicted SPOUT methyltransferase (SPOUT_MTase)	Predicted SPOUT methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D], C [auth A], D [auth B]	Ribosomal RNA large subunit methyltransferase H	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity RNA methyltransferase activity rRNA methyltransferase activity rRNA (pseudouridine-N3-)-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 identical protein binding protein binding binding protein homodimerization activity protein dimerization activity RNA methyltransferase activity rRNA methyltransferase activity rRNA (pseudouridine-N3-)-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 rRNA (pseudouridine) methyltransferase activity methyltransferase activity catalytic activity ribonucleoprotein complex binding protein-containing complex binding ribosome 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	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth D], C [auth A], D [auth B]	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A [auth C], B [auth D], C [auth A], D [auth B]	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A [auth C], B [auth D], C [auth A], D [auth B]	IPR003742	RNA methyltransferase RlmH	Family

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.