Any feedback?
Information on EC 2.1.1.182 - 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase and Organism(s) Escherichia coli and UniProt Accession P06992
for references in articles please use BRENDA:EC2.1.1.182Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
2.1.1.182 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferaseIUBMB Comments
KsgA introduces the most highly conserved ribosomal RNA modification, the dimethylation of adenine1518 and adenine1519 in 16S rRNA. Strains lacking the methylase are resistant to kasugamycin .
Specify your search results
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Reaction Schemes
4
+
=
4
+
4
+
adenine1518/adenine1519 in 16S rRNA
=
4
+
N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
Synonyms
ksga methyltransferase, s-adenosylmethionine-6-n',n'-adenosyl (rrna) dimethyltransferase, 16s rrna adenine dimethyltransferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA = 4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
reaction mechanism, overview
-
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
KsgA introduces the most highly conserved ribosomal RNA modification, the dimethylation of adenine1518 and adenine1519 in 16S rRNA. Strains lacking the methylase are resistant to kasugamycin [1].
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
4 S-adenosyl-L-methionine + adenine1518/1519 in 18S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 18S rRNA
-
methylation of Escherichia coli 30S ribosomes. Under assay conditions the enzyme produces both N6-methyladenine and N6-dimethyladenine, with 0.8times as much N6-methyladenine as N6-dimethyladenine
-
-
?
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
-
-
-
?
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
4 methyl groups are incorporated per 16S RNA molecule, both adenine residues in the 16S RNA sequence AACCUG are dimethylated
-
-
?
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
dimethylates the adenine residues in 16S rRNA-derived oligonucleotide with the specific sequence AACCUG
-
-
?
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
dimethylation of AI518 and A1519 in the hairpin loop of 16S rRNA. Site-specific mutagenesis of 16S rRNA of Escherichia coli ribosomes is used to make five mutations around the highly conserved UI512-GI523 base pair in the 3'-terminal hairpin. G1523 and C1524 in the stem are important determinants for the dimethylation of A1518 and AI519 in the loop
-
-
?
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
neither of the adenine residues is required for methylation of the other, ruling out any obligate order of methylation of A1518 and A1519. Mutation of either A1518 or A1519 to C, G or U has little effect on the ability of the mutant RNA to reconstitute a 30S ribosome containing a full complement of ribosomal proteins
-
-
?
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
recombinant KsgA is able to efficiently methylate 30S subunits isolated from strains of Escherichia coli resistant to kasugamycin, but not wild-type 30S subunits, indicating that the methylation function is specific for A1518 and A1519. KsgA is unable to utilize 30S subunits in the translationally active state as a substrate
-
-
?
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
binding of 30S subunit and S-adenosyl-L-methionine, structure, overview. After the S-adenosyl-L-methionine addition, KsgA dissociates rapidly from the subunits. The binding of KsgA to substrate is complex and requires regions of rRNA well beyond helix 45, including regions of the 790 loop
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA
4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
additional information
-
K+ and NH4+ in the range of 10 to 150 mM have little effect on methylation
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
protein S21
-
S21 probably inhibits KsgA activity in an indirect way, presumably by stabilizing 30S in a conformation that for whatever reason cannot be methylated by KsgA
-
additional information
-
a mixture of 30 S ribosomal proteins inhibits methylation of mutant 30 S ribosomes. This inhibition can be ascribed to ribosomal protein S21. Initiation factor 3 partially inhibits methylation of mutant 30 S ribosomes
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
KM-value for S-adenosylmethionine is in the range 0.002-0.007 mM
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Escherichia coli
-
IC50 values of unlabeled wild-type or mutant protein competing with fluorescently labeled wild-type protein for binding to 30S subunits
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
cold sensitivity and altered ribosomal profiles are associated with a DELTAksgA genotype in Escherichia coli
physiological function
evolution
-
the KsgA family belongs tothe group of S-adenosyl-L-methionine-dependent methyltransferases, known as class I MTases, KsgA is related to DNA adenosine methyltransferases, which transfer only a single methyl group to their target adenosine residue. Part of the discrimination between mono- and dimethyltransferase activity lies in a single residue in the active site, L114; this residue is part of a conserved motif, known as motif IV, which is common to a large group of S-adenosyl-L-methionine-dependent methyltransferases
malfunction
physiological function
physiological function
KsgA acts as a ribosome biogenesis factor. KsgA alters 16S rRNA processing and has a critical role is as a supervisor of biogenesis of 30S subunits in vivo
physiological function
KsgA has a DNA glycosylase/AP lyase activity for C mispaired with oxidized T that prevents the formation of mutations, which is in addition to its rRNA adenine methyltransferase activity essential for ribosome biogenesis
malfunction
-
the inability to form dimethyladenine in the 16S rRNA-derived oligonucleotide is accompanied by muatation from kasugamycin sensitivity to resistance
malfunction
-
yeast enzyme Dim1 complements heterologously for ksgA- mutation in Escherichia coli, demonstrating functional equivalence of the two proteins
physiological function
-
KsgA, in addition to its methyltransferase activity, has another unidentified function that plays a role in the suppression of the cold-sensitive phenotype of the Era(E200K) strain. The additional function may be involved in the acid shock response
physiological function
-
the KsgA methyltransferase is universally conserved and plays a key role in regulating ribosome biogenesis. KsgA has a complex reaction mechanism, transferring a total of four methyl groups onto two separate adenosine residues, A1518 and A1519, in the small subunit rRNA. This means that the active site pocket must accept both adenosine and N6-methyladenosine as substrates to catalyze formation of the final product N6,N6-dimethyladenosine
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C168A
-
site-directed mutagenesis, the mutation does not affect KsgA activity
E43A
-
mutation located in the S-adenosylmethionine-binding motifs severely reduces methyltransferase activity, the mutation retains the ability to suppress the growth defect of the Era(E200K) strain at a low temperature
E66A
-
mutation located in the S-adenosylmethionine-binding motifs severely reduces methyltransferase activity, the mutation retains the ability to suppress the growth defect of the Era(E200K) strain at a low temperature
G47A
-
mutation located in the S-adenosylmethionine-binding motifs severely reduces methyltransferase activity, the mutation retains the ability to suppress the growth defect of the Era(E200K) strain at a low temperature
L114P
-
site-directed mutagenesis of the active site residue, the KsgA mutant shows diminished overall activity, and impaired ability to methylate the N6-methyladenosine intermediate to produce N6,N6-dimethyladenosine. Reduced activity is not due to disruption of 30S substrate binding
N113A
-
site-directed mutagenesis of the active site residue, the KsgA mutant shows diminishes activity to a level comparable to L114P without affecting the methylation of N6-methyladenosine. Reduced activity is not due to disruption of 30S substrate binding
R248A
-
mutation at the C-terminal does not affect the methyltransferase activity and fails to suppress the growth defect of the Era(E200K) strain
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes from Escherichia coli strain XL1-Blue
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
KsgA engineered with an N-terminal polyhistidine tag is overexpressed in Escherichia coli cells
expression of wild-type and mutant enzymes in Escherichia coli strain XL1-Blue
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Formenoy, L.J.; Cunningham, P.R.; Nurse, K.; Pleij, C.W.A.; Ofengand, J.
Methylation of the conserved A1518-A1519 in Escherichia coli 16S ribosomal RNA by the ksgA methyltransferase is influenced by methylations around the similarly conserved U1512-G1523 base pair in the 3' terminal hairpin
Biochimie
76
1123-1128
1994
Escherichia coli
O'Farrell, H.C.; Scarsdale, J.N.; Rife, J.P.
Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli
J. Mol. Biol.
339
337-353
2004
Escherichia coli (P06992)
Desai, P.M.; Rife, J.P.
The adenosine dimethyltransferase KsgA recognizes a specific conformational state of the 30S ribosomal subunit
Arch. Biochem. Biophys.
449
57-63
2006
Escherichia coli
Cunningham, P.R.; Weitzmann, C.J.; Nurse, K.; Masurel, R.; van Knippenberg, P.H.; Ofengand, J.
Site-specific mutation of the conserved m6(2)A m6(2)A residues of E. coli 16S ribosomal RNA. Effects on ribosome function and activity of the ksgA methyltransferase
Biochim. Biophys. Acta
1050
18-26
1990
Escherichia coli
van Buul, C.P.; van Knippenberg, P.H.
Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA
Gene
38
65-72
1985
Escherichia coli (P06992)
Inoue, K.; Basu, S.; Inouye, M.
Dissection of 16S rRNA methyltransferase (KsgA) function in Escherichia coli
J. Bacteriol.
189
8510-8518
2007
Escherichia coli
Poldermans, B.; Roza, L.; van Knippenberg, P.H.
Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions
J. Biol. Chem.
254
9094-9100
1979
Escherichia coli
Lafontaine, D.; Delcour, J.; Glasser, A.L.; Desgres, J.; Vandenhaute, J.
The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3'-terminal loop of 18 S rRNA is essential in yeast
J. Mol. Biol.
241
492-497
1994
Escherichia coli
Andresson, O.S.; Davies, J.E.
Some properties of the ribosomal RNA methyltransferase encoded by ksgA and the polarity of ksgA transcription
Mol. Gen. Genet.
179
217-222
1980
Escherichia coli
Connolly, K.; Rife, J.P.; Culver, G.
Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA
Mol. Microbiol.
70
1062-1075
2008
Escherichia coli (P06992)
Helser, T.L.; Davies, J.E.; Dahlberg, J.E.
Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli
Nat. New Biol.
233
12-14
1971
Escherichia coli
Helser, T.L.; Davies, J.E.; Dahlberg, J.E.
Mechanism of kasugamycin resistance in Escherichia coli
Nat. New Biol.
235
6-9
1972
Escherichia coli
Zhang-Akiyama, Q.M.; Morinaga, H.; Kikuchi, M.; Yonekura, S.; Sugiyama, H.; Yamamoto, K.; Yonei, S.
KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli
Nucleic Acids Res.
37
2116-2125
2009
Escherichia coli (P06992)
O'Farrell, H.C.; Pulicherla, N.; Desai, P.M.; Rife, J.P.
Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution
RNA
12
725-733
2006
Escherichia coli
EXTERNAL LINKS (specific for EC-Number 2.1.1.182)
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
