1YUB | pdb_00001yub

SOLUTION STRUCTURE OF AN RRNA METHYLTRANSFERASE (ERMAM) THAT CONFERS MACROLIDE-LINCOSAMIDE-STREPTOGRAMIN ANTIBIOTIC RESISTANCE, NMR, MINIMIZED AVERAGE STRUCTURE

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD 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	d1yuba_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	rRNA adenine dimethylase-like	rRNA adenine dimethylase	(Streptococcus pneumoniae ) [TaxId: 1313 ],	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, catalytic domain-like	8019907	4003608	SCOP2 (2022-06-29)
A	SCOP2 Family	rRNA adenine dimethylase, C-terminal domain-like	8090729	4007710	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032287	3000118	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S13-like H2TH domain	8090730	3000053	SCOP2 (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	RrnaAD_C_1	e1yubA1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: RrnaAD_C_1	ECOD (1.6)
A	RrnaAD_N	e1yubA2	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	1.10.8.100	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A	ARO:3000375	ErmB	ErmB confers the MLSb phenotype. Similar to ErmC, expression of ErmB is inducible by erythromycin. The leader peptide causes attenuation of the mRNA and stabilizes the structure preventing further translation. When erythromycin is present, it binds the leader peptide causing a change in conformation allowing for the expression of ErmB.	CARD (4.0.1)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A	ARO:3000560	Erm 23S ribosomal RNA methyltransferase	macrolide antibiotic, lincosamide antibiotic, streptogramin antibiotic, streptogramin A antibiotic, streptogramin B antibiotic	antibiotic target alteration	CARD (4.0.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RRNA METHYLTRANSFERASE	23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity 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 rRNA (adenine-N6-)-methyltransferase activity N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity 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 rRNA (adenine-N6-)-methyltransferase activity N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity RNA binding binding nucleic acid binding rRNA (adenine-N6,N6-)-dimethyltransferase activity	response to stimulus response to chemical response to antibiotic	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001737	Ribosomal RNA adenine methyltransferase KsgA/Erm	Family
A	IPR020598	Ribosomal RNA adenine methylase transferase, N-terminal	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR023165	rRNA adenine dimethylase-like, C-terminal	Homologous Superfamily
A	IPR020596	Ribosomal RNA adenine methylase transferase, conserved site	Conserved 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.