Ribosomal RNA small subunit methyltransferase A - Escherichia coli (strain K12)

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P06992 (RSMA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 111. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ribosomal RNA small subunit methyltransferase A
EC=2.1.1.182

Alternative name(s):
16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase
16S rRNA dimethyladenosine transferase
16S rRNA dimethylase
High level kasugamycin resistance protein ksgA
Kasugamycin dimethyltransferase
S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase

Gene names

Name:	rsmA
Synonyms:	ksgA
Ordered Locus Names:	b0051, JW0050

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	273 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Specifically dimethylates two adjacent adenosines (A1518 and A1519) in the loop of a conserved hairpin near the 3'-end of 16S rRNA in the 30S particle. May play a critical role in biogenesis of 30S subunits. Has also a DNA glycosylase/AP lyase activity that removes C mispaired with oxidized T from DNA, and may play a role in protection of DNA against oxidative stress. Ref.1 Ref.8 Ref.11
Catalytic activity	4 S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1518)/N(6)-dimethyladenine(1519) in 16S rRNA. HAMAP MF_00607
Subcellular location	Cytoplasm Potential HAMAP MF_00607.
Disruption phenotype	Inactivation leads to kasugamycin resistance. Cells lacking this gene show cold-sensitivity phenotype, altered ribosome profiles, and small subunit rRNA-processing defects. Ref.1 Ref.11
Miscellaneous	When overexpressed partially suppresses the slow growth and decreased 70S ribosome phenotype of an rsgA knockout; RsgA may be involved in 30S ribosomal subunit biogenesis. Upon overexpression also restores cold-sensitive growth of a missense mutation in Era. HAMAP MF_00607
Sequence similarities	Belongs to the methyltransferase superfamily. rRNA adenine N(6)-methyltransferase family. RsmA subfamily.

Ontologies

Keywords
Biological process	Antibiotic resistance rRNA processing
Cellular component	Cytoplasm
Ligand	RNA-binding S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	rRNA base methylation Inferred from mutant phenotype. Source: EcoCyc response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW ribosomal small subunit assembly Inferred from mutant phenotype Ref.11. Source: EcoCyc
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	double-stranded DNA binding Inferred from direct assay. Source: EcoCyc mRNA binding Inferred from direct assay. Source: EcoCyc rRNA (adenine-N6,N6-)-dimethyltransferase activity Inferred from direct assay. Source: EcoCyc rRNA binding Inferred from direct assay. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.8

Chain

2 – 273

272

Ribosomal RNA small subunit methyltransferase A HAMAP MF_00607

PRO_0000101524

Sites

Binding site

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

S-adenosyl-L-methionine; via amide nitrogen By similarity

Binding site

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

S-adenosyl-L-methionine By similarity

Binding site

S-adenosyl-L-methionine By similarity

Binding site

113

S-adenosyl-L-methionine By similarity

Experimental info

Mutagenesis

E → A: Loss of activity. Overexpression of the mutant has a negative effect on cell growth, probably because it sequesters the small subunits in the free form and limits their participation in the translation cycle. Ref.11

Secondary structure

273

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P06992 [UniParc].

Last modified April 1, 1988. Version 1.
Checksum: BBB163A0F4011C9D
Show »

FASTA

273

30,420

        10         20         30         40         50         60 
MNNRVHQGHL ARKRFGQNFL NDQFVIDSIV SAINPQKGQA MVEIGPGLAA LTEPVGERLD 

        70         80         90        100        110        120 
QLTVIELDRD LAARLQTHPF LGPKLTIYQQ DAMTFNFGEL AEKMGQPLRV FGNLPYNIST 

       130        140        150        160        170        180 
PLMFHLFSYT DAIADMHFML QKEVVNRLVA GPNSKAYGRL SVMAQYYCNV IPVLEVPPSA 

       190        200        210        220        230        240 
FTPPPKVDSA VVRLVPHATM PHPVKDVRVL SRITTEAFNQ RRKTIRNSLG NLFSVEVLTG 

       250        260        270 
MGIDPAMRAE NISVAQYCQM ANYLAENAPL QES

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA." van Buul C.P.J.J., van Knippenberg P.H. Gene 38:65-72(1985) [PubMed: 3905517] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, DISRUPTION PHENOTYPE.
[2]	"The gene for Escherichia coli diadenosine tetraphosphatase is located immediately clockwise to folA and forms an operon with ksgA." Blanchin-Roland S., Blanquet S., Schmitter J.-M., Fayat G. Mol. Gen. Genet. 205:515-522(1986) [PubMed: 3031429] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region." Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Nucleic Acids Res. 20:3305-3308(1992) [PubMed: 1630901] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12." Roa B.B., Connolly D.M., Winkler M.E. J. Bacteriol. 171:4767-4777(1989) [PubMed: 2670894] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-62. Strain: K12.
[7]	"Characterization of the ksgA gene of Escherichia coli determining kasugamycin sensitivity." van Gemen B., Koets H.J., Plooy C.A.M., Bodlaender J., van Knippenberg P.H. Biochimie 69:841-848(1987) [PubMed: 3122846] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-67.
[8]	"KsgA, a 16S rRNA adenine methyltransferase, has a novel DNA glycosylase/AP lyase activity to prevent mutations in Escherichia coli." Zhang-Akiyama Q.M., Morinaga H., Kikuchi M., Yonekura S., Sugiyama H., Yamamoto K., Yonei S. Nucleic Acids Res. 37:2116-2125(2009) [PubMed: 19223326] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-11, FUNCTION AS A DNA GLYCOSYLASE/AP LYASE.
[9]	"The gene for 16S rRNA methyltransferase (ksgA) functions as a multicopy suppressor for a cold-sensitive mutant of era, an essential RAS-like GTP-binding protein in Escherichia coli." Lu Q., Inouye M. J. Bacteriol. 180:5243-5246(1998) [PubMed: 9748462] [Abstract] Cited for: SUPPRESSES AN ERA MUTANT.
[10]	"Genetic interaction screens with ordered overexpression and deletion clone sets implicate the Escherichia coli GTPase YjeQ in late ribosome biogenesis." Campbell T.L., Brown E.D. J. Bacteriol. 190:2537-2545(2008) [PubMed: 18223068] [Abstract] Cited for: PARTIALLY SUPPRESSES AN RSGA DISRUPTION MUTANT. Strain: K12.
[11]	"Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA." Connolly K., Rife J.P., Culver G. Mol. Microbiol. 70:1062-1075(2008) [PubMed: 18990185] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLU-66.
[12]	"Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli." O'Farrell H.C., Scarsdale J.N., Rife J.P. J. Mol. Biol. 339:337-353(2004) [PubMed: 15136037] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 17-268.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M11054 Genomic DNA. Translation: AAA24049.1.
X04711 Genomic DNA. Translation: CAA28417.1.
U00096 Genomic DNA. Translation: AAC73162.1.
AP009048 Genomic DNA. Translation: BAE76038.1.
M68521 Genomic DNA. Translation: AAA24306.1.
X06536 Genomic DNA. Translation: CAA29786.1.

PIR

XYECRO. A24527.

RefSeq

NP_414593.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QYR	X-ray	2.10	A/B	17-268	[»]

ProteinModelPortal

P06992.

SMR

P06992. Positions 17-268.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10076N.

IntAct

P06992. 4 interactions.

MINT

MINT-1246440.

2D gel databases

ECO2DBASE

H025.2. 6TH EDITION.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000002260; EBESCP00000002260; EBESCG00000001852.
EBESCT00000002261; EBESCP00000002261; EBESCG00000001852.
EBESCT00000002262; EBESCP00000002262; EBESCG00000001852.
EBESCT00000002263; EBESCP00000002263; EBESCG00000001852.
EBESCT00000018417; EBESCP00000017708; EBESCG00000017471.

GeneID

944939.

GenomeReviews

Gene locus JW0050 in contig AP009048_GR.
Gene locus b0051 in contig U00096_GR.

KEGG

ecj:JW0050.
eco:b0051.

PATRIC

32115201. VBIEscCol129921_0052.

Organism-specific databases

EchoBASE

EB0518.

EcoGene

EG10523. rsmA.

Phylogenomic databases

eggNOG

COG0030.

GeneTree

EBGT00050000011735.

HOGENOM

HBG319664.

OMA

LPHPAKD.

PhylomeDB

P06992.

ProtClustDB

PRK00274.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10523-MONOMER.
MetaCyc:EG10523-MONOMER.

BRENDA

2.1.1.48. 2026.

Gene expression databases

Genevestigator

P06992.

Family and domain databases

HAMAP

MF_00607. 16SrRNA_methyltr_A.
[Tree]

InterPro

IPR023165. rRNA_Ade_diMease-like.
IPR020596. rRNA_Ade_Mease_Trfase_CS.
IPR001737. rRNA_Ade_methylase_transferase.
IPR020598. rRNA_Ade_methylase_Trfase_N.
IPR011530. rRNA_adenine_dimethylase.
[Graphical view]

Gene3D

G3DSA:1.10.8.100. rRNA_Ade_diMease-like. 1 hit.

K02528.

PANTHER

PTHR11727. RRNA_meth_trans. 1 hit.

Pfam

PF00398. RrnaAD. 1 hit.
[Graphical view]

SMART

SM00650. rADc. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00755. KsgA. 1 hit.

PROSITE

PS01131. RRNA_A_DIMETH. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RSMA_ECOLI

Accession

Primary (citable) accession number: P06992
Secondary accession number(s): Q2MCG8

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	April 1, 1988
Last modified:	January 25, 2012
This is version 111 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents