3R9X

Crystal structure of Era in complex with MgGDPNP, nucleotides 1506-1542 of 16S ribosomal RNA, and KsgA

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	d3r9xb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Prokaryotic type KH domain (KH-domain type II)	8089833	3001043	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8089831	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8073146	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S13-like H2TH domain	8090720	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	KH_2	e3r9xA1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_2	ECOD (1.6)
A	MnmE_helical_2nd	e3r9xA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
B	RrnaAD_C	e3r9xB2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: RrnaAD_C	ECOD (1.6)
B	RrnaAD_N	e3r9xB1	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	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, 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	1.10.8.100	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	PF01926	50S ribosome-binding GTPase (MMR_HSR1)	50S ribosome-binding GTPase	-	Family
A	PF07650	KH domain (KH_2)	KH domain	-	Domain
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	GTPase Era	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding small ribosomal subunit rRNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding small ribosomal subunit rRNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ribonucleoprotein complex binding protein-containing complex binding ribosomal small subunit binding ribosome binding	ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis ribosome assembly	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane
C	RNA301	-	-	-
B	Ribosomal RNA small subunit methyltransferase A	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 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic 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 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity RNA binding binding organic cyclic compound binding nucleic acid 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 RNA methylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR030388	Era-type guanine nucleotide-binding (G) domain	Domain
A	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
A	IPR004044	K Homology domain, type 2	Domain
A	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
A	IPR005662	GTPase Era	Family
A	IPR005225	Small GTP-binding protein domain	Domain
A	IPR006073	GTP binding domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR001737	Ribosomal RNA adenine methyltransferase KsgA/Erm	Family
B	IPR020598	Ribosomal RNA adenine methylase transferase, N-terminal	Domain
B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B	IPR023165	rRNA adenine dimethylase-like, C-terminal	Homologous Superfamily
B	IPR011530	Ribosomal RNA adenine dimethylase	Family
B	IPR020596	Ribosomal RNA adenine methylase transferase, conserved site	Conserved 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.