ID   RSMA_ECOLI              Reviewed;         273 AA.
AC   P06992; Q2MCG8;
DT   01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-APR-1988, sequence version 1.
DT   02-SEP-2026, entry version 197.
DE   RecName: Full=Ribosomal RNA small subunit methyltransferase A;
DE            EC=2.1.1.182;
DE   AltName: Full=16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase;
DE   AltName: Full=16S rRNA dimethyladenosine transferase;
DE   AltName: Full=16S rRNA dimethylase;
DE   AltName: Full=High level kasugamycin resistance protein KsgA;
DE   AltName: Full=Kasugamycin dimethyltransferase;
DE   AltName: Full=S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase;
GN   Name=rsmA; Synonyms=ksgA; OrderedLocusNames=b0051, JW0050;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=3905517; DOI=10.1016/0378-1119(85)90204-5;
RA   van Buul C.P.J.J., van Knippenberg P.H.;
RT   "Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of
RT   methyltransferases effecting dimethylation of adenosine in ribosomal RNA.";
RL   Gene 38:65-72(1985).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=3031429; DOI=10.1007/bf00338091;
RA   Blanchin-Roland S., Blanquet S., Schmitter J.-M., Fayat G.;
RT   "The gene for Escherichia coli diadenosine tetraphosphatase is located
RT   immediately clockwise to folA and forms an operon with ksgA.";
RL   Mol. Gen. Genet. 205:515-522(1986).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=1630901; DOI=10.1093/nar/20.13.3305;
RA   Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K.,
RA   Mizobuchi K., Nakata A.;
RT   "Systematic sequencing of the Escherichia coli genome: analysis of the
RT   0-2.4 min region.";
RL   Nucleic Acids Res. 20:3305-3308(1992).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-62.
RC   STRAIN=K12;
RX   PubMed=2670894; DOI=10.1128/jb.171.9.4767-4777.1989;
RA   Roa B.B., Connolly D.M., Winkler M.E.;
RT   "Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of
RT   Escherichia coli K-12.";
RL   J. Bacteriol. 171:4767-4777(1989).
RN   [7]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-67.
RX   PubMed=3122846; DOI=10.1016/0300-9084(87)90210-0;
RA   van Gemen B., Koets H.J., Plooy C.A.M., Bodlaender J.,
RA   van Knippenberg P.H.;
RT   "Characterization of the ksgA gene of Escherichia coli determining
RT   kasugamycin sensitivity.";
RL   Biochimie 69:841-848(1987).
RN   [8]
RP   PROTEIN SEQUENCE OF 2-11, AND FUNCTION AS A DNA GLYCOSYLASE/AP LYASE.
RX   PubMed=19223326; DOI=10.1093/nar/gkp057;
RA   Zhang-Akiyama Q.M., Morinaga H., Kikuchi M., Yonekura S., Sugiyama H.,
RA   Yamamoto K., Yonei S.;
RT   "KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP
RT   lyase activity to prevent mutations in Escherichia coli.";
RL   Nucleic Acids Res. 37:2116-2125(2009).
RN   [9]
RP   IDENTIFICATION BY 2D-GEL.
RX   PubMed=9298644; DOI=10.1002/elps.1150180805;
RA   VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT   "Escherichia coli proteome analysis using the gene-protein database.";
RL   Electrophoresis 18:1243-1251(1997).
RN   [10]
RP   SUPPRESSES AN ERA MUTANT.
RX   PubMed=9748462; DOI=10.1128/jb.180.19.5243-5246.1998;
RA   Lu Q., Inouye M.;
RT   "The gene for 16S rRNA methyltransferase (ksgA) functions as a multicopy
RT   suppressor for a cold-sensitive mutant of era, an essential RAS-like GTP-
RT   binding protein in Escherichia coli.";
RL   J. Bacteriol. 180:5243-5246(1998).
RN   [11]
RP   PARTIALLY SUPPRESSES AN RSGA DISRUPTION MUTANT.
RC   STRAIN=K12;
RX   PubMed=18223068; DOI=10.1128/jb.01744-07;
RA   Campbell T.L., Brown E.D.;
RT   "Genetic interaction screens with ordered overexpression and deletion clone
RT   sets implicate the Escherichia coli GTPase YjeQ in late ribosome
RT   biogenesis.";
RL   J. Bacteriol. 190:2537-2545(2008).
RN   [12]
RP   FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLU-66.
RX   PubMed=18990185; DOI=10.1111/j.1365-2958.2008.06485.x;
RA   Connolly K., Rife J.P., Culver G.;
RT   "Mechanistic insight into the ribosome biogenesis functions of the ancient
RT   protein KsgA.";
RL   Mol. Microbiol. 70:1062-1075(2008).
RN   [13]
RP   X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 17-268.
RX   PubMed=15136037; DOI=10.1016/j.jmb.2004.02.068;
RA   O'Farrell H.C., Scarsdale J.N., Rife J.P.;
RT   "Crystal structure of KsgA, a universally conserved rRNA adenine
RT   dimethyltransferase in Escherichia coli.";
RL   J. Mol. Biol. 339:337-353(2004).
RN   [14]
RP   STRUCTURE BY ELECTRON MICROSCOPY (13.5 ANGSTROMS) OF 17-268 IN COMPLEX WITH
RP   THE 30S RIBOSOMAL SMALL SUBUNIT, AND RNA-BINDING.
RX   PubMed=22308031; DOI=10.1074/jbc.m111.318121;
RA   Boehringer D., O'Farrell H.C., Rife J.P., Ban N.;
RT   "Structural insights into methyltransferase KsgA function in 30S ribosomal
RT   subunit biogenesis.";
RL   J. Biol. Chem. 287:10453-10459(2012).
CC   -!- FUNCTION: Specifically dimethylates two adjacent adenosines (A1518 and
CC       A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA
CC       in the 30S particle. May play a critical role in biogenesis of 30S
CC       subunits. Also has a DNA glycosylase/AP lyase activity that removes C
CC       mispaired with oxidized T from DNA, and may play a role in protection
CC       of DNA against oxidative stress. {ECO:0000269|PubMed:18990185,
CC       ECO:0000269|PubMed:19223326, ECO:0000269|PubMed:3905517}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=adenosine(1518)/adenosine(1519) in 16S rRNA + 4 S-adenosyl-L-
CC         methionine = N(6)-dimethyladenosine(1518)/N(6)-
CC         dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine + 4
CC         H(+); Xref=Rhea:RHEA:19609, Rhea:RHEA-COMP:10232, Rhea:RHEA-
CC         COMP:10233, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:74411, ChEBI:CHEBI:74493; EC=2.1.1.182;
CC   -!- INTERACTION:
CC       P06992; P0A8A8: rimP; NbExp=2; IntAct=EBI-1113369, EBI-561065;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC   -!- DISRUPTION PHENOTYPE: Inactivation leads to kasugamycin resistance.
CC       Cells lacking this gene show cold-sensitivity phenotype, altered
CC       ribosome profiles, and small subunit rRNA-processing defects.
CC       {ECO:0000269|PubMed:18990185, ECO:0000269|PubMed:3905517}.
CC   -!- MISCELLANEOUS: When overexpressed partially suppresses the slow growth
CC       and decreased 70S ribosome phenotype of an rsgA knockout; RsgA may be
CC       involved in 30S ribosomal subunit biogenesis. Upon overexpression also
CC       restores cold-sensitive growth of a missense mutation in Era.
CC   -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC       superfamily. rRNA adenine N(6)-methyltransferase family. RsmA
CC       subfamily. {ECO:0000305}.
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DR   EMBL; M11054; AAA24049.1; -; Genomic_DNA.
DR   EMBL; X04711; CAA28417.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC73162.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE76038.1; -; Genomic_DNA.
DR   EMBL; M68521; AAA24306.1; -; Genomic_DNA.
DR   EMBL; X06536; CAA29786.1; -; Genomic_DNA.
DR   PIR; A24527; XYECRO.
DR   RefSeq; NP_414593.1; NC_000913.3.
DR   RefSeq; WP_001065381.1; NZ_CP009789.1.
DR   PDB; 1QYR; X-ray; 2.10 A; A/B=17-268.
DR   PDB; 3TPZ; X-ray; 2.10 A; A/B=1-273.
DR   PDB; 4ADV; EM; 13.50 A; V=17-268.
DR   PDB; 7AFO; EM; 3.93 A; Y=1-273.
DR   PDB; 7NAW; EM; 4.05 A; Y=1-273.
DR   PDB; 7O5H; EM; 3.10 A; V=17-268.
DR   PDB; 8EYT; EM; 2.80 A; W=15-268.
DR   AlphaFoldDB; P06992; -.
DR   EMDB; EMD-2017; -.
DR   SMR; P06992; -.
DR   BioGRID; 4261012; 76.
DR   FunCoup; P06992; 746.
DR   IntAct; P06992; 5.
DR   STRING; 511145.b0051; -.
DR   jPOST; P06992; -.
DR   PaxDb; 511145-b0051; -.
DR   EnsemblBacteria; AAC73162; AAC73162; b0051.
DR   GeneID; 93777384; -.
DR   GeneID; 944939; -.
DR   KEGG; ecj:JW0050; -.
DR   KEGG; eco:b0051; -.
DR   KEGG; ecoc:C3026_00265; -.
DR   PATRIC; fig|1411691.4.peg.2232; -.
DR   EchoBASE; EB0518; -.
DR   eggNOG; COG0030; Bacteria.
DR   HOGENOM; CLU_041220_0_1_6; -.
DR   InParanoid; P06992; -.
DR   OMA; GMFQKEV; -.
DR   OrthoDB; 9814755at2; -.
DR   PhylomeDB; P06992; -.
DR   BioCyc; EcoCyc:EG10523-MONOMER; -.
DR   BioCyc; MetaCyc:EG10523-MONOMER; -.
DR   BRENDA; 2.1.1.182; 2026.
DR   EvolutionaryTrace; P06992; -.
DR   PRO; PR:P06992; -.
DR   Proteomes; UP000000625; Chromosome.
DR   AbasyAtlas; P06992; -.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0052908; F:16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity; IDA:EcoCyc.
DR   GO; GO:0003690; F:double-stranded DNA binding; IDA:EcoCyc.
DR   GO; GO:0003729; F:mRNA binding; IDA:EcoCyc.
DR   GO; GO:0043024; F:ribosomal small subunit binding; IDA:EcoCyc.
DR   GO; GO:0000179; F:rRNA (adenine-N6,N6-)-dimethyltransferase activity; IDA:EcoCyc.
DR   GO; GO:0030490; P:maturation of SSU-rRNA; IGI:EcoCyc.
DR   GO; GO:0000028; P:ribosomal small subunit assembly; IMP:EcoCyc.
DR   GO; GO:0070475; P:rRNA base methylation; IMP:EcoCyc.
DR   GO; GO:0031167; P:rRNA methylation; IBA:GO_Central.
DR   GO; GO:0006364; P:rRNA processing; IMP:EcoCyc.
DR   FunFam; 1.10.8.100:FF:000001; Ribosomal RNA small subunit methyltransferase A; 1.
DR   FunFam; 3.40.50.150:FF:000006; Ribosomal RNA small subunit methyltransferase A; 1.
DR   Gene3D; 1.10.8.100; Ribosomal RNA adenine dimethylase-like, domain 2; 1.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR   HAMAP; MF_00607; 16SrRNA_methyltr_A; 1.
DR   InterPro; IPR001737; KsgA/Erm.
DR   InterPro; IPR023165; rRNA_Ade_diMease-like_C.
DR   InterPro; IPR020596; rRNA_Ade_Mease_Trfase_CS.
DR   InterPro; IPR020598; rRNA_Ade_methylase_Trfase_N.
DR   InterPro; IPR011530; rRNA_adenine_dimethylase.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   NCBIfam; TIGR00755; ksgA; 1.
DR   PANTHER; PTHR11727; DIMETHYLADENOSINE TRANSFERASE; 1.
DR   PANTHER; PTHR11727:SF7; DIMETHYLADENOSINE TRANSFERASE-RELATED; 1.
DR   Pfam; PF00398; RrnaAD; 1.
DR   SMART; SM00650; rADc; 1.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR   PROSITE; PS01131; RRNA_A_DIMETH; 1.
DR   PROSITE; PS51689; SAM_RNA_A_N6_MT; 1.
DR   PDBsum; 1QYR; -.
DR   PDBsum; 3TPZ; -.
DR   PDBsum; 4ADV; -.
DR   PDBsum; 7AFO; -.
DR   PDBsum; 7NAW; -.
DR   PDBsum; 7O5H; -.
DR   PDBsum; 8EYT; -.
PE   1: Evidence at protein level;
KW   3D-structure; Antibiotic resistance; Cytoplasm; Direct protein sequencing;
KW   Methyltransferase; Reference proteome; RNA-binding; rRNA processing;
KW   S-adenosyl-L-methionine; Transferase.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000269|PubMed:19223326"
FT   CHAIN           2..273
FT                   /note="Ribosomal RNA small subunit methyltransferase A"
FT                   /id="PRO_0000101524"
FT   BINDING         18
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         20
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         45
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         66
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         91
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   BINDING         113
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000250"
FT   MUTAGEN         66
FT                   /note="E->A: Loss of activity. Overexpression of the mutant
FT                   has a negative effect on cell growth, probably because it
FT                   sequesters the small subunits in the free form and limits
FT                   their participation in the translation cycle."
FT                   /evidence="ECO:0000269|PubMed:18990185"
FT   HELIX           9..11
FT                   /evidence="ECO:0007829|PDB:3TPZ"
FT   HELIX           23..33
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          37..39
FT                   /evidence="ECO:0007829|PDB:7O5H"
FT   STRAND          41..44
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   TURN            47..51
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           52..56
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          62..65
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           69..76
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   TURN            79..81
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           82..84
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          85..88
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           92..94
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           97..104
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          108..113
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   TURN            116..118
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           119..127
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           130..132
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          133..141
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           142..149
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          152..156
FT                   /evidence="ECO:0007829|PDB:3TPZ"
FT   HELIX           159..167
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          168..176
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           178..180
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          181..183
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   STRAND          189..196
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           207..219
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   TURN            220..222
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           225..228
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   TURN            229..232
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           235..240
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           249..251
FT                   /evidence="ECO:0007829|PDB:1QYR"
FT   HELIX           254..267
FT                   /evidence="ECO:0007829|PDB:1QYR"
SQ   SEQUENCE   273 AA;  30420 MW;  BBB163A0F4011C9D CRC64;
     MNNRVHQGHL ARKRFGQNFL NDQFVIDSIV SAINPQKGQA MVEIGPGLAA LTEPVGERLD
     QLTVIELDRD LAARLQTHPF LGPKLTIYQQ DAMTFNFGEL AEKMGQPLRV FGNLPYNIST
     PLMFHLFSYT DAIADMHFML QKEVVNRLVA GPNSKAYGRL SVMAQYYCNV IPVLEVPPSA
     FTPPPKVDSA VVRLVPHATM PHPVKDVRVL SRITTEAFNQ RRKTIRNSLG NLFSVEVLTG
     MGIDPAMRAE NISVAQYCQM ANYLAENAPL QES
//