Information on EC 2.1.1.184 - 23S rRNA (adenine2085-N6)-dimethyltransferase

Word Map on EC 2.1.1.184
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)

The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
2.1.1.184
-
RECOMMENDED NAME
GeneOntology No.
23S rRNA (adenine2085-N6)-dimethyltransferase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2 S-adenosyl-L-methionine + adenine2085 in 23S rRNA = 2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
show the reaction diagram
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:23S rRNA (adenine2085-N6)-dimethyltransferase
ErmC is a methyltransferase that confers resistance to the macrolide-lincosamide-streptogramin B group of antibiotics by catalysing the methylation of 23S rRNA at adenine2085.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain BD1167 carrying naturally occurring plasmid pIM13 with ermC' gene
SwissProt
Manually annotated by BRENDA team
strain BD170 carrying plasmid pE194-cop-1 with the ermC gene
SwissProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2 S-adenosyl-L-methionine + adenine2085 in 23S rRNA
2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
show the reaction diagram
2 S-adenosyl-L-methionine + adenine2085 in a 262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
show the reaction diagram
-
a 262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA can be utilized efficiently as a substrate for methylation at adenine2085
-
-
?
2 S-adenosyl-L-methionine + adenine2085 in a 623-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in a 623-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
show the reaction diagram
-
-
-
-
?
2 S-adenosyl-L-methionine + adenine2085 in a 623-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA with mutation A2086T
2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in a 623-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA with mutation A2086T
show the reaction diagram
-
the A2086T change is methylated to ca. 50% of the level of wild-type domain V
-
-
?
S-adenosyl-L-methionine + adenine2085 in 23S rRNA
S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
show the reaction diagram
-
adenine2085 in 23S rRNA from Bacillus subtilis equals adenine2058 in Escherichia coli 23S rRNA
-
-
?
additional information
?
-
-
direct autoregulatory mechanism operating at the posttranscriptional level and independently of the ermC methylase-mediated methylation of ribosomes. A translational repression model is suggested in which the ermC methyltransferase binds to its own mRNA, at a region that resembles the methylation target site on 23S rRNA
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2 S-adenosyl-L-methionine + adenine2085 in 23S rRNA
2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
show the reaction diagram
S-adenosyl-L-methionine + adenine2085 in 23S rRNA
S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
show the reaction diagram
-
adenine2085 in 23S rRNA from Bacillus subtilis equals adenine2058 in Escherichia coli 23S rRNA
-
-
?
additional information
?
-
-
direct autoregulatory mechanism operating at the posttranscriptional level and independently of the ermC methylase-mediated methylation of ribosomes. A translational repression model is suggested in which the ermC methyltransferase binds to its own mRNA, at a region that resembles the methylation target site on 23S rRNA
-
-
-
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-([[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl][3-(1H-imidazol-1-yl)propyl]amino]methyl)-1H-isoindole-1,3(2H)-dione
i.e. PD00556
4-methyl-2,6-di[(4-methylphenyl)thio]nicotinonitrile
i.e. RF00667
N6-dimethyladenine2085 containing 23S rRNA
linear competitive inhibition kinetics with RNA as the variable substrate, mixed inhibition with S-adenosyl-L-methionine as the variable substrate
-
nicotinaldehyde-N-[3-(2-chlorobenzyl)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-7-yl]hydrazone
i.e. HTS12610
S-adenosyl-L-homocysteine
sinefungin
-
competitive
additional information
the crystal structure of ErmC methyltransferase is used as a target for structure-based virtual screening of a database composed of 58679 lead-like compounds. Among 77 compounds selected for experimental validation (63 predicted to bind to the catalytic pocket and 14 compounds predicted to bind to the putative RNA binding site), several novel inhibitors are found that decrease the minimal inhibitory concentration of a macrolide antibiotic erythromycin toward an Escherichia coli strain that constitutively expresses ErmC'. Analysis of docking models of the identified inhibitors suggests a novel strategy to develop potent and clinically useful inhibitors
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0000375
23S rRNA
-
pH 7.5, 37C, a 262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
-
0.00091
262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
-
pH 7.5, 37C, a 262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
-
0.0000344
623-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
-
pH 7.5, 37C, a 262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
-
0.000144
623-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA with mutation A2086T
-
pH 7.5, 37C, a 262-nucleotide RNA fragment within domain V of Bacillus subtilis 23S rRNA
-
0.0003 - 0.012
adenine2085 in 23S rRNA
-
0.000354 - 0.0257
S-adenosyl-L-methionine
additional information
additional information
-
interaction between 23s rRNA and ermC' methyltransferase. Kinetic and thermodynamic parameters of binding are determined
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00011 - 2.2
adenine2085 in 23S rRNA
-
0.0121 - 0.0775
S-adenosyl-L-methionine
additional information
additional information
Bacillus subtilis
-
interaction between 23s rRNA and ermC' methyltransferase. Kinetic and thermodynamic parameters of binding are determined
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.066 - 914
adenine2085 in 23S rRNA
1489
0.67 - 23.6
S-adenosyl-L-methionine
24
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000128 - 0.00036
N6-dimethyladenine2085 containing 23S rRNA
-
0.033 - 0.086
S-adenosyl-L-homocysteine
0.018
sinefungin
-
pH 7.5, 21C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.3
2-([[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl][3-(1H-imidazol-1-yl)propyl]amino]methyl)-1H-isoindole-1,3(2H)-dione
Bacillus subtilis
P13956
pH 7.5, 25C
0.18
4-methyl-2,6-di[(4-methylphenyl)thio]nicotinonitrile
Bacillus subtilis
P13956
pH 7.5, 25C
0.25
nicotinaldehyde-N-[3-(2-chlorobenzyl)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-7-yl]hydrazone
Bacillus subtilis
P13956
pH 7.5, 25C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallized by the hanging drop vapor diffusion method. Structure of the apo-enzyme at 2.2 A resolution. The crystal structures of ErmC' and of its complexes with the cofactor S-adenosyl-L-methionine, the reaction product S-adenosyl-L-homocysteine and the methyltransferase inhibitor sinefungin, respectively, show that the enzyme undergoes small conformational changes upon ligand binding
-
crystals of ErmC' are obtained by the hanging-drop vapor diffusion method. Crystal structure of ErmC' (a naturally occurring variant of ErmC) determined at 3.0 A resolution by multiple anomalous diffraction phasing methods. The structure consists of a conserved alpha/beta amino-terminal domain which binds the cofactor S-adenosyl-L-methionine, followed by a smaller, alpha-helical RNA-recognition domain
-
the crystal structure of ErmC methyltransferase is used as a target for structure-based virtual screening of a database composed of 58679 lead-like compounds. Analysis of docking models of the identified inhibitors suggests a novel strategy to develop potent and clinically useful inhibitors
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BW25113B cells fused to green fluorescent protein
-
expressed to a high level in Escherichia coli
-
expression in Escherichia coli
the expression of ErmC' by translational coupling to kdsB, under the control of the T7lac promoter. The pTERM31 plasmid is transformed into Escherichia coli strain BL219(DE3)/pLysS
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
direct autoregulatory mechanism operating at the posttranscriptional level and independently of the ermC methylase-mediated methylation of ribosomes. A translational repression model is suggested in which the ermC methyltransferase binds to its own mRNA, at a region that resembles the methylation target site on 23S rRNA
-
induction is due to a posttranscriptional mechanism in which the inducer activates translation of methylase mRNA by binding to unmethylated (erythromycin-sensitive) ribosomes and stalling them in the leader region. Pseudomonic acid A can also induce methylase synthesis. Isoleucine starvation has a similar effect on ribosomes translating the ermC leader region to cause induction of methylase synthesis. Requirement for ribosome stalling and destabilization of a stem-loop structure and demonstration that stalling can occur without macrolide-bound ribosomes
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E128A
-
kcat/KM for S-adenosyl-L-methionine is 46% of wild type value. kcat/KM for RNA is 59% of wild type value. No difference in generating erythromycin resistance when compared to the wild-type enzyme
E202A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 32% of the wild-type value. kcat/Km for RNA is 40% of wild-type value
F163A
-
kcat/KM for S-adenosyl-L-methionine is 67% of wild type value. kcat/KM for RNA is 28% of wild type value. Mutant enzyme still mediates erythromycin resistance, although at reduced level
K133A
-
decreased ability in rendering DH5alpha cells resistant to erythromycin, suggesting that this amino acid is not absolutely indispensable for the ErmC' activity, but might be involved in important RNA-protein interactions. No change in affinity towards the RNA substrate. kcat/Km for S-adenosyl-L-methionine is% of the wild-type value. kcat/Km for RNA is 27% of wild-type value. kcat/Km for S-adenosyl-L-methionine is 13% of the wild-type value. kcat/Km for RNA is% of wild-type value
K166A
-
kcat/KM for S-adenosyl-L-methionine is 74% of wild type value. kcat/KM for RNA is 58% of wild type value. Little difference in generating erythromycin resistance when compared to the wild-type enzyme
K168A
-
kcat/KM for S-adenosyl-L-methionine is 59% of wild type value. kcat/KM for RNA is 70% of wild type value. No difference in generating erythromycin resistance when compared to the wild-type enzyme
K197A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 67% of the wild-type value. kcat/Km for RNA is 50% of wild-type value
K197A/N200A/E202A/K204A/K205A
-
the five mutations together do not show a visible cumulative effect on the ErmC' activity in vivo
K204A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 73% of the wild-type value. kcat/Km for RNA is 89% of wild-type value
K205A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 63% of the wild-type value. kcat/Km for RNA is 92% of wild-type value
K209A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 72% of the wild-type value. kcat/Km for RNA is 73% of wild-type value
M196A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 42% of the wild-type value. kcat/Km for RNA is 56% of wild-type value
N101A
-
kcat/KM for S-adenosyl-L-methionine is 10% of wild type value. kcat/KM for RNA is 11% of wild type value. Mutant enzyme is totally unable to render DH5alpha cells resistant to erythromycin
N11A
-
kcat/KM for S-adenosyl-L-methionine is 32% of wild type value. kcat/KM for RNA is 33% of wild type value. Little difference in generating erythromycin resistance when compared to the wild-type enzyme
N192A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 73% of the wild-type value. kcat/Km for RNA is 74% of wild-type value
N200A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 42% of the wild-type value. kcat/Km for RNA is 54% of wild-type value
P165A
-
kcat/KM for S-adenosyl-L-methionine is 4% of wild type value. kcat/KM for RNA is 4% of wild type value. Mutant enzyme still mediates erythromycin resistance, although at reduced level
R112A
-
decreased ability in rendering DH5alpha cells resistant to erythromycin, suggesting that this amino acid is not absolutely indispensable for the ErmC' activity, but might be involved in important RNA-protein interactions. kcat/Km for S-adenosyl-L-methionine is 12% of the wild-type value. kcat/Km for RNA is 7% of wild-type value
R112D
-
decreased ability in rendering DH5alpha cells resistant to erythromycin. The R112D mutant shows a more pronounced decrease in RNA-binding affinity compared with R112A. kcat/Km for S-adenosyl-L-methionine is 5% of the wild-type value. kcat/Km for RNA is 2% of wild-type value
R134A
-
mutant exhibits the most severe effect on the ErmC' ability to generate erythromycin resistance, this mutant has completely lost the activity in vivo. kcat/Km for S-adenosyl-L-methionine is 3% of the wild-type value. kcat/Km for RNA is 1% of wild-type value
R140A
-
decreased ability in rendering DH5alpha cells resistant to erythromycin, suggesting that this amino acid is not absolutely indispensable for the ErmC' activity, but might be involved in important RNA-protein interactions. kcat/Km for S-adenosyl-L-methionine is 1% of the wild-type value. kcat/Km for RNA is 3% of wild-type value
T108A
-
decreased ability in rendering DH5alpha cells resistant to erythromycin, suggesting that this amino acid is not absolutely indispensable for the ErmC' activity, but might be involved in important RNA-protein interactions. kcat/Km for S-adenosyl-L-methionine is 4% of the wild-type value. kcat/Km for RNA is 3% of wild-type value
Y104A
-
mutant enzyme is totally unable to render DH5alpha cells resistant to erythromycin
E128A
-
kcat/KM for S-adenosyl-L-methionine is 46% of wild type value. kcat/KM for RNA is 59% of wild type value. No difference in generating erythromycin resistance when compared to the wild-type enzyme
-
E202A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 32% of the wild-type value. kcat/Km for RNA is 40% of wild-type value
-
K133A
-
decreased ability in rendering DH5alpha cells resistant to erythromycin, suggesting that this amino acid is not absolutely indispensable for the ErmC' activity, but might be involved in important RNA-protein interactions. No change in affinity towards the RNA substrate. kcat/Km for S-adenosyl-L-methionine is% of the wild-type value. kcat/Km for RNA is 27% of wild-type value. kcat/Km for S-adenosyl-L-methionine is 13% of the wild-type value. kcat/Km for RNA is% of wild-type value
-
K168A
-
kcat/KM for S-adenosyl-L-methionine is 59% of wild type value. kcat/KM for RNA is 70% of wild type value. No difference in generating erythromycin resistance when compared to the wild-type enzyme
-
K197A
-
mutant of a residues positioned on the surface of the small domain, does not display substantial defects in activity compared with the wild-type enzyme. kcat/Km for S-adenosyl-L-methionine is 67% of the wild-type value. kcat/Km for RNA is 50% of wild-type value
-
N11A
-
kcat/KM for S-adenosyl-L-methionine is 32% of wild type value. kcat/KM for RNA is 33% of wild type value. Little difference in generating erythromycin resistance when compared to the wild-type enzyme
-
R112A
-
decreased ability in rendering DH5alpha cells resistant to erythromycin, suggesting that this amino acid is not absolutely indispensable for the ErmC' activity, but might be involved in important RNA-protein interactions. kcat/Km for S-adenosyl-L-methionine is 12% of the wild-type value. kcat/Km for RNA is 7% of wild-type value
-
Y104A
-
mutant enzyme is totally unable to render DH5alpha cells resistant to erythromycin
-
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine