RSMA_ECOLI
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 03-AUG-2022, entry version 180.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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 0-
RT 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. Has also 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 = 4 H(+) + N(6)-dimethyladenosine(1518)/N(6)-
CC dimethyladenosine(1519) in 16S rRNA + 4 S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:19609, Rhea:RHEA-COMP:10232, Rhea:RHEA-COMP:10233,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74493; EC=2.1.1.182;
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_STEB01000010.1.
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; 7O5H; EM; 3.10 A; V=17-268.
DR PDBsum; 1QYR; -.
DR PDBsum; 3TPZ; -.
DR PDBsum; 4ADV; -.
DR PDBsum; 7AFO; -.
DR PDBsum; 7O5H; -.
DR AlphaFoldDB; P06992; -.
DR SMR; P06992; -.
DR BioGRID; 4261012; 72.
DR IntAct; P06992; 4.
DR STRING; 511145.b0051; -.
DR jPOST; P06992; -.
DR PaxDb; P06992; -.
DR PRIDE; P06992; -.
DR EnsemblBacteria; AAC73162; AAC73162; b0051.
DR EnsemblBacteria; BAE76038; BAE76038; BAE76038.
DR GeneID; 66671659; -.
DR GeneID; 944939; -.
DR KEGG; ecj:JW0050; -.
DR KEGG; eco:b0051; -.
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; KEEEPYF; -.
DR PhylomeDB; P06992; -.
DR BioCyc; EcoCyc:EG10523-MON; -.
DR BioCyc; MetaCyc:EG10523-MON; -.
DR BRENDA; 2.1.1.182; 2026.
DR EvolutionaryTrace; P06992; -.
DR PRO; PR:P06992; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
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:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
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 Gene3D; 1.10.8.100; -; 1.
DR Gene3D; 3.40.50.150; -; 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 PANTHER; PTHR11727; PTHR11727; 1.
DR Pfam; PF00398; RrnaAD; 1.
DR SMART; SM00650; rADc; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00755; ksgA; 1.
DR PROSITE; PS01131; RRNA_A_DIMETH; 1.
DR PROSITE; PS51689; SAM_RNA_A_N6_MT; 1.
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 128..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
