P13956 (ERM_BACIU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
rRNA adenine N-6-methyltransferase
EC=2.1.1.184

Alternative name(s):
Erythromycin resistance protein
Macrolide-lincosamide-streptogramin B resistance protein

Gene names

Name:

ermC'

Encoded on

Plasmid pIM13

Organism

Bacillus subtilis

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group

Protein attributes

Sequence length	244 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.3 Ref.4
Catalytic activity	2 S-adenosyl-L-methionine + adenine(2085) in 23S rRNA = 2 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(2085) in 23S rRNA.
Sequence similarities	Belongs to the methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family.
Caution	In the genome of Neisseria meningitidis (serogroup B), the gene for this protein is present (NMB0066). It was introduced as part of a construct built to neutralize the virulence of the bacterium.

Ontologies

Keywords
Biological process	Antibiotic resistance
Ligand	RNA-binding S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
Technical term	3D-structure Plasmid
Gene Ontology (GO)
Biological_process	rRNA methylation Inferred from electronic annotation. Source: GOC response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity Inferred from electronic annotation. Source: EC RNA binding Inferred from electronic annotation. Source: UniProtKB-KW rRNA (adenine-N6,N6-)-dimethyltransferase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 244

244

rRNA adenine N-6-methyltransferase

PRO_0000101674

Sites

Binding site

11

1

S-adenosyl-L-methionine; via carbonyl oxygen

Binding site

13

1

S-adenosyl-L-methionine; via amide nitrogen

Binding site

38

1

S-adenosyl-L-methionine; via carbonyl oxygen

Binding site

59

1

S-adenosyl-L-methionine

Binding site

84

1

S-adenosyl-L-methionine

Binding site

101

1

S-adenosyl-L-methionine

Experimental info

Mutagenesis

11

1

N → A: Reduces activity about 3-fold.

Mutagenesis

101

1

N → A: Decreases affinity for S-adenosyl-L-methionine 4-fold. Reduces activity by 90%. Ref.3

Mutagenesis

104

1

Y → A: Loss of activity. Ref.3

Mutagenesis

108

1

T → A: Decreases affinity for S-adenosyl-L-methionine 8-fold. Reduces activity by 99%. Ref.4

Mutagenesis

112

1

R → A: Reduces activity by 90%. Ref.4

Mutagenesis

112

1

R → D: Decreases affinity for S-adenosyl-L-methionine 5-fold. Decreases affinity for RNA 6-fold. Reduces activity by 99%. Ref.4

Mutagenesis

133

1

K → A: Reduces activity by about 80%. Ref.4

Mutagenesis

134

1

R → A: Decreases affinity for S-adenosyl-L-methionine 7-fold. Decreases affinity for RNA about 4-fold. Reduces activity by over 99%. May severely impair protein folding. Ref.4

Mutagenesis

140

1

R → A: Decreases affinity for S-adenosyl-L-methionine 7-fold. Reduces activity by about 85%. Ref.4

Mutagenesis

165

1

P → A: Decreases affinity for S-adenosyl-L-methionine 6-fold. Reduces activity by about 96%. Ref.3

Mutagenesis

166

1

K → A: Decreases affinity for RNA about 6-fold. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

244

Helix Strand Turn

Details...

Helix

16 – 23

8

Beta strand

33 – 37

5

Helix

43 – 51

9

Beta strand

52 – 58

7

Helix

62 – 71

10

Turn

72 – 74

3

Beta strand

77 – 81

5

Helix

85 – 87

3

Beta strand

92 – 94

3

Beta strand

97 – 101

5

Helix

104 – 106

3

Helix

107 – 116

10

Beta strand

121 – 128

8

Helix

129 – 135

7

Beta strand

138 – 140

3

Helix

141 – 146

6

Turn

147 – 149

3

Beta strand

150 – 158

9

Helix

160 – 162

3

Beta strand

163 – 165

3

Beta strand

171 – 178

8

Helix

185 – 187

3

Helix

188 – 199

12

Helix

203 – 205

3

Helix

209 – 219

11

Helix

229 – 242

14

Sequences

	Sequence		Length	Mass (Da)
	P13956 [UniParc]. Last modified January 1, 1990. Version 1. Checksum: FC7CA6524034D820	FASTA	244	28,907
	10 20 30 40 50 60 MNEKNIKHSQ NFITSKHNID KIMTNIRLNE HDNIFEIGSG KGHFTLELVQ RCNFVTAIEI 70 80 90 100 110 120 DHKLCKTTEN KLVDHDNFQV LNKDILQFKF PKNQSYKIFG NIPYNISTDI IRKIVFDSIA 130 140 150 160 170 180 DEIYLIVEYG FAKRLLNTKR SLALFLMAEV DISILSMVPR EYFHPKPKVN SSLIRLNRKK 190 200 210 220 230 240 SRISHKDKQK YNYFVMKWVN KEYKKIFTKN QFNNSLKHAG IDDLNNISFE QFLSLFNSYK LFNK

References

[1]	"Sequence and properties of pIM13, a macrolide-lincosamide-streptogramin B resistance plasmid from Bacillus subtilis." Monod M., Denoya C., Dubnau D. J. Bacteriol. 167:138-147(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Substrate requirements for ErmC' methyltransferase activity." Zhong P., Pratt S.D., Edalji R.P., Walter K.A., Holzman T.F., Shivakumar A.G., Katz L. J. Bacteriol. 177:4327-4332(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION.
[3]	"Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'." Maravic G., Feder M., Pongor S., Floegel M., Bujnicki J.M. J. Mol. Biol. 332:99-109(2003) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASN-101; TYR-104; PRO-165 AND LYS-166, RNA-BINDING, FUNCTION.
[4]	"Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions." Maravic G., Bujnicki J.M., Feder M., Pongor S., Floegel M. Nucleic Acids Res. 31:4941-4949(2003) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF THR-108; ARG-112; LYS-133; ARG-134 AND ARG-140, RNA-BINDING, FUNCTION.
[5]	"Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria." Bussiere D.E., Muchmore S.W., Dealwis C.G., Schluckebier G., Nienaber V.L., Edalji R.P., Walter K.A., Ladror U.S., Holzman T.F., Abad-Zapatero C. Biochemistry 37:7103-7112(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 10-244. Strain: BD1109.
[6]	"The 2.2-A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism." Schluckebier G., Zhong P., Stewart K.D., Kavanaugh T.J., Abad-Zapatero C. J. Mol. Biol. 289:277-291(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH S-ADENOSYL-L-METHIONINE AND SUBSTRATE ANALOGS.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M13761 Genomic DNA. Translation: AAA98136.1.

PIR

B25233.

RefSeq

NP_040407.1. NC_001376.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QAM	X-ray	2.20	A	1-244	[»]
1QAN	X-ray	2.40	A	1-244	[»]
1QAO	X-ray	2.70	A	1-244	[»]
1QAQ	X-ray	2.80	A	1-244	[»]
2ERC	X-ray	3.03	A/B	1-244	[»]

ProteinModelPortal

P13956.

SMR

P13956. Positions 9-244.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1263203.

Phylogenomic databases

ProtClustDB

CLSK884354.

Family and domain databases

Gene3D

1.10.8.100. 1 hit.

InterPro

IPR023165. rRNA_Ade_diMease-like.
IPR020596. rRNA_Ade_Mease_Trfase_CS.
IPR001737. rRNA_Ade_methylase_transferase.
IPR020598. rRNA_Ade_methylase_Trfase_N.
[Graphical view]

PANTHER

PTHR11727. PTHR11727. 1 hit.

Pfam

PF00398. RrnaAD. 1 hit.
[Graphical view]

SMART

SM00650. rADc. 1 hit.
[Graphical view]

PROSITE

PS01131. RRNA_A_DIMETH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P13956.

ChEMBL

CHEMBL4251.

EvolutionaryTrace

P13956.

Entry information

Entry name

ERM_BACIU

Accession

Primary (citable) accession number: P13956

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 1, 1990
Last modified:	April 3, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program