1ZQ9

Crystal structure of human Dimethyladenosine transferase

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1zq9a1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	rRNA adenine dimethylase-like	Probable dimethyladenosine transferase	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1zq9b_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	rRNA adenine dimethylase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	rRNA adenine dimethylase C-terminal domain-like	8090727	4007710	SCOP2 (2022-06-29)
A	SCOP2 Family	rRNA adenine dimethylase catalytic domain-like	8023757	4003608	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S13-like H2TH domain	8090728	3000053	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8036137	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8036137	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S13-like H2TH domain	8090728	3000053	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	PTZ00338	e1zq9A2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: PTZ00338	ECOD (1.6)
A	RrnaAD_N	e1zq9A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: RrnaAD_N	ECOD (1.6)
B	PTZ00338	e1zq9B2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: PTZ00338	ECOD (1.6)
B	RrnaAD_N	e1zq9B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: RrnaAD_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	1.10.8.480	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	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	1.10.8.480	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00398	Ribosomal RNA adenine dimethylase (RrnaAD)	Ribosomal RNA adenine dimethylase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable dimethyladenosine transferase	RNA methyltransferase activity rRNA (adenine-N6,N6-)-dimethyltransferase 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 N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity RNA methyltransferase activity rRNA (adenine-N6,N6-)-dimethyltransferase 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 N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity RNA binding binding organic cyclic compound binding nucleic acid binding	ribonucleoprotein complex biogenesis regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis positive regulation of metabolic process ribosome biogenesis regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process ribonucleoprotein complex biogenesis regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis positive regulation of metabolic process ribosome biogenesis regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process ncRNA metabolic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process cellular process macromolecule metabolic process regulation of metabolic process ribosomal small subunit biogenesis rRNA methylation rRNA modification macromolecule methylation RNA modification methylation macromolecule modification RNA methylation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle preribosome protein-containing complex ribonucleoprotein complex small-subunit processome cytoplasm cytosol nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001737	Ribosomal RNA adenine methyltransferase KsgA/Erm	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR020598	Ribosomal RNA adenine methylase transferase, N-terminal	Domain
A, B	IPR011530	Ribosomal RNA adenine dimethylase	Family
A, B	IPR020596	Ribosomal RNA adenine methylase transferase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UNQ2	lymphoplasmacytic lymphoma Sjogren syndrome osteosarcoma plasma cell myeloma

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.