1QAM

THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM

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
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1qama_	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	(Bacillus subtilis ) [TaxId: 1423 ],	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	8090703	4007710	SCOP2 (2022-06-29)
A	SCOP2 Family	rRNA adenine dimethylase catalytic domain-like	8019906	4003608	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S13-like H2TH domain	8090704	3000053	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032286	3000118	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	PF00398	e1qamA2	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: PF00398	ECOD (1.6)
A	PF00398	e1qamA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF00398	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:3000250	ErmC	ErmC is a methyltransferase that catalyzes the methylation of A2058 of the 23S ribosomal RNA in two steps. Expression of ErmC 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 ErmC.	CARD (3.2.9)

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 (3.2.9)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	ERMC' 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 organic cyclic compound binding nucleic acid binding rRNA (adenine-N6,N6-)-dimethyltransferase activity	response to stimulus response to chemical response to antibiotic	-

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

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	23S rRNA (adenine2085-N6)-dimethyltransferase M-CSA #898	This protein produces a dimethylation of the adenine residue at position 2085 in 23S rRNA, resulting in reduced affinity between ribosomes and macrolide-lincosamide-streptogramin B antibiotics.	Defined by 5 residues: GLY:A-38GLU:A-59ASN:A-101TYR:A-104PHE:A-163 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.48 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.48

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.