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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	rsmA
Gene Synonym(s)	ECK0052, b0051, JW0050, rsmA, ksgA^[1]^[2], ksgA
Product Desc.	S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase^[3]^[2] 16S rRNA dimethyladenosine transferase; S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase; mutant is kasugamycin resistant; multicopy suppressor of era(Cs)^[4]
Product Synonyms(s)	S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase^[1], B0051^[3]^[1], KsgA^[3]^[1], RsmA^[3]^[1] , ECK0052, JW0050, ksgA, b0051
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pdxA-rsmA^[3], pdxA-rsmA, pdxA-rsmA-apaGH^[3], pdxA-rsmA-apaG-apaH, rsmA-apaGH^[3], rsmA-apaG-apaH, rsmA-apaG-apaH, surA-pdxA-rsmA-apaGH^[3], surA-pdxA-rsmA-apaGH
Regulation/Activity
Quick Links
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Notes

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KsgA dimethylates two adjacent 16S rRNA adenosines. ksgA deletion mutants grow more slowly than an isogenic wt at 20C (Connolly, 2008).^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	rsmA
Mnemonic	Ribosomal Small subunit Methyltransferase
Synonyms	ECK0052, b0051, JW0050, rsmA, ksgA^[1]^[2], ksgA
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	1.11 minutes	MG1655: 52430..51609 <gbrowseImage> name=NC_000913:51609..52430 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 55804..56625 <gbrowseImage> name=NC_012967:55804..56625 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 51609..52430 <gbrowseImage> name=NC_012759:51609..52430 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 52430..51609 <gbrowseImage> name=NC_007779:51609..52430 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 52430..51609 <gbrowseImage> name=NC_010473:51609..52430 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ksgA(del) (Keio:JW0050)	deletion	deletion			PMID:16738554	Shigen CGSC8292^[5]
rsmAE66A		E66A		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			seeded from UniProt:P06992
ksgA23						CGSC:8757
ksgA19						CGSC:10346
ksgA40						CGSC:91435
ksgA2					PMID:6256606	CGSC:91441
ksgA4						CGSC:91444
ksgA733(del)::kan					PMID:16738554	CGSC:99630
ksgA23 ksgB1			Resistant to	Double mutant is Resistant to Kasugamycin at levels greater than 2,000 µg/ml.	PMID:4570603	Strain: FS157 parental: CSGC	See table 5 for resistance.
ksgA19			Resistant to	Resistant to Aminoglycoside Kasugamycin at concentrations at 1,000 µg/ml.	PMID:4570603	Strain: FS232 Parental: JC411	See table 5
ksgA19			Resistant to	Resistant to Aminoglycoside Kasugamycin at concentrations at 2,000 µg/ml.	PMID:4570603	Strain: FS131 Parental: JC12	See table 5
ksgA23			Resistant to	Resistant to the Aminoglycoside Kasugamycin at concentrations of 100 µg/ml.	PMID:4570603	Parental: JC411 Strain: FS215	Table 5.
ksgA23			Resistant to	Resistant to the Aminoglycoside Kasugamycin at concentrations of 500 µg/ml.	PMID:4570603	Parental: CGSC:8757 Strain: FS233	Table 5.
pUC8ksgA5			Resistant to	Resistance to Kasugamycin	PMID:3905517	Parental Strain: Q13
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW0050	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATAATCGAGTCCACCAGGG Primer 2:CCACTCTCCTGCAAAGGCGCGTT
2F7	Kohara Phage	Genobase	PMID:3038334
4A3	Kohara Phage	Genobase	PMID:3038334
8D2	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 50% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 28% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0051
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0064
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:KSGA
CGSC (EcoliWiki Page)	CGSC:583
EcoCyc (EcoliWiki Page)	ECOCYC:EG10523	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944939	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	RsmA
Synonyms	S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase^[1], B0051^[3]^[1], KsgA^[3]^[1], RsmA^[3]^[1] , ECK0052, JW0050, ksgA, b0051
Product description	S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase^[3]^[2] 16S rRNA dimethyladenosine transferase; S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase; mutant is kasugamycin resistant; multicopy suppressor of era(Cs)^[4]
EC number (for enzymes)	2.1.1.-^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0000179	rRNA (adenine-N6,N6-)-dimethyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001737	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000179	rRNA (adenine-N6,N6-)-dimethyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020596	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000179	rRNA (adenine-N6,N6-)-dimethyltransferase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020598	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00607	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0046677	response to antibiotic	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0046	P	Seeded from EcoCyc (v14.0)	complete
	GO:0070475	rRNA base methylation	PMID:4567337	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	murB	PMID:16606699	Experiment(s):EBI-1135454
Protein	guaA	PMID:16606699	Experiment(s):EBI-1135454
Protein	groL	PMID:16606699	Experiment(s):EBI-1135454
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
cytoplasm			From EcoCyc^[2]
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc 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
Length	273
Mol. Wt	30.419 kDa
pI	8.1 (calculated)
Extinction coefficient	11,920 - 12,170 (calc based on 8 Y, W, and 2 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Domain	8..266	PF00398 Ribosomal RNA adenine dimethylase		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ksgA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16128045	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944939	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P06992	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944939	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
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Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	3312	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	500	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	1600	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
pdxA-rsmA
pdxA-rsmA-apaGH
rsmA-apaGH
surA-pdxA-rsmA-apaGH
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File:.jpg

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:52410..52450 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0051 (EcoliWiki Page)	NCBI GEO profiles for ksgA
microarray	GenExpDB:b0051 (EcoliWiki Page)	Summary of data for ksgA from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to rsmA Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0051
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000016944 (score: 1.000; bootstrap: 64%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000023168 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G66360 (score: 1.000; bootstrap: 76%) AT2G47420 (score: 0.289)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000015680 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00032987 (score: 1.000; bootstrap: 49%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00020189 (score: 1.000; bootstrap: 52%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000000817 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000008063 (score: 1.000; bootstrap: 65%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040801-75 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040801-82 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0186850 (score: 1.000; bootstrap: 73%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0039627 (score: 1.000; bootstrap: 57%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA20255-PA (score: 1.000; bootstrap: 50%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000022157 (score: 1.000; bootstrap: 66%)	From Inparanoid:20070104
Homo sapiens	ENSP00000031512 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000014624 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000010150 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Mus musculus	MGI:2146851 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Oryza gramene	Q6Z4B0 (score: 1.000; bootstrap: 100%) Q8SAZ2 (score: 0.074) Q7G6D5 (score: 0.074)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000031966 (score: 1.000; bootstrap: 76%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000022397 (score: 1.000; bootstrap: 73%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YPL266W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC3362 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000139638 (score: 1.000; bootstrap: 67%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00028675001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000017166 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Shigella flexneri	KSGA	From SHIGELLACYC
E. coli O157	KSGA	From ECOO157CYC
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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
Panther (EcoliWiki Page)	PTHR11727:SF7
Pfam (EcoliWiki Page)	PF00398 Ribosomal RNA adenine dimethylase
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

rsmA:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to rsmA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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