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Protein

Ribosomal RNA small subunit methyltransferase F

Gene

rsmF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + cytosine(1407) in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(1407) in 16S rRNA.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei149 – 1491S-adenosyl-L-methionineBy similarity
Binding sitei176 – 1761S-adenosyl-L-methionineBy similarity
Binding sitei194 – 1941S-adenosyl-L-methionineBy similarity
Active sitei247 – 2471NucleophileBy similarity

GO - Molecular functioni

  • RNA binding Source: UniProtKB-KW
  • rRNA (cytosine-C5-)-methyltransferase activity Source: EcoCyc

GO - Biological processi

  • rRNA base methylation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:G7008-MONOMER.
ECOL316407:JW5301-MONOMER.
MetaCyc:G7008-MONOMER.
BRENDAi2.1.1.178. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA small subunit methyltransferase F (EC:2.1.1.178)
Alternative name(s):
16S rRNA m5C1407 methyltransferase
rRNA (cytosine-C(5)-)-methyltransferase RsmF
Gene namesi
Name:rsmF
Synonyms:yebU
Ordered Locus Names:b1835, JW5301
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14023. rsmF.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 479479Ribosomal RNA small subunit methyltransferase FPRO_0000211822Add
BLAST

Proteomic databases

PaxDbiP76273.
PRIDEiP76273.

Interactioni

Protein-protein interaction databases

BioGridi4259158. 9 interactions.
STRINGi511145.b1835.

Structurei

Secondary structure

1
479
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 167Combined sources
Helixi17 – 193Combined sources
Helixi27 – 337Combined sources
Beta strandi41 – 433Combined sources
Turni45 – 473Combined sources
Helixi50 – 578Combined sources
Helixi58 – 603Combined sources
Beta strandi70 – 745Combined sources
Helixi86 – 883Combined sources
Helixi90 – 934Combined sources
Beta strandi96 – 994Combined sources
Helixi102 – 11110Combined sources
Turni112 – 1154Combined sources
Beta strandi119 – 1257Combined sources
Helixi130 – 1389Combined sources
Turni139 – 1413Combined sources
Beta strandi143 – 1486Combined sources
Helixi152 – 16514Combined sources
Beta strandi169 – 1735Combined sources
Helixi180 – 1834Combined sources
Beta strandi188 – 1947Combined sources
Helixi200 – 2045Combined sources
Beta strandi209 – 2124Combined sources
Helixi215 – 23521Combined sources
Beta strandi236 – 24712Combined sources
Turni252 – 2543Combined sources
Helixi255 – 26410Combined sources
Turni266 – 2683Combined sources
Beta strandi269 – 2713Combined sources
Helixi281 – 2844Combined sources
Beta strandi291 – 2933Combined sources
Turni295 – 2995Combined sources
Beta strandi303 – 3108Combined sources
Helixi334 – 34512Combined sources
Turni346 – 3483Combined sources
Beta strandi355 – 36814Combined sources
Helixi369 – 3746Combined sources
Beta strandi381 – 39111Combined sources
Beta strandi394 – 3974Combined sources
Helixi399 – 4057Combined sources
Beta strandi408 – 4158Combined sources
Helixi418 – 4258Combined sources
Beta strandi439 – 4457Combined sources
Beta strandi448 – 4547Combined sources
Turni456 – 4594Combined sources
Helixi466 – 4683Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FRXX-ray2.90A/B/C/D1-479[»]
ProteinModelPortaliP76273.
SMRiP76273. Positions 7-474.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP76273.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni125 – 1317S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CYJ. Bacteria.
COG0144. LUCA.
COG3270. LUCA.
HOGENOMiHOG000218115.
InParanoidiP76273.
KOiK11392.
OMAiWCAEGFW.
OrthoDBiEOG6091D0.
PhylomeDBiP76273.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01579. 16SrRNA_methyltr_F.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR031341. Methyltr_RsmF_N.
IPR001678. MeTrfase_RsmB/NOP2.
IPR027391. Nol1_Nop2_Fmu_2.
IPR011023. Nop2p.
IPR023267. RCMT.
IPR023545. rRNA_ssu_MeTfrase_F.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
PF17125. Methyltr_RsmF_N. 1 hit.
PF13636. Methyltranf_PUA. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00446. nop2p. 1 hit.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P76273-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQHTVYFPD AFLTQMREAM PSTLSFDDFL AACQRPLRRS IRVNTLKISV
60 70 80 90 100
ADFLQLTAPY GWTLTPIPWC EEGFWIERDN EDALPLGSTA EHLSGLFYIQ
110 120 130 140 150
EASSMLPVAA LFADGNAPQR VMDVAAAPGS KTTQISARMN NEGAILANEF
160 170 180 190 200
SASRVKVLHA NISRCGISNV ALTHFDGRVF GAAVPEMFDA ILLDAPCSGE
210 220 230 240 250
GVVRKDPDAL KNWSPESNQE IAATQRELID SAFHALRPGG TLVYSTCTLN
260 270 280 290 300
QEENEAVCLW LKETYPDAVE FLPLGDLFPG ANKALTEEGF LHVFPQIYDC
310 320 330 340 350
EGFFVARLRK TQAIPALPAP KYKVGNFPFS PVKDREAGQI RQAATGVGLN
360 370 380 390 400
WDENLRLWQR DKELWLFPVG IEALIGKVRF SRLGIKLAET HNKGYRWQHE
410 420 430 440 450
AVIALASPDN MNAFELTPQE AEEWYRGRDV YPQAAPVADD VLVTFQHQPI
460 470
GLAKRIGSRL KNSYPRELVR DGKLFTGNA
Length:479
Mass (Da):53,228
Last modified:December 15, 1998 - v2
Checksum:i30D2B6AD01FCFF3E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74905.2.
AP009048 Genomic DNA. Translation: BAA15648.2.
PIRiC64945.
RefSeqiNP_416349.2. NC_000913.3.
WP_001352260.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74905; AAC74905; b1835.
BAA15648; BAA15648; BAA15648.
GeneIDi946348.
KEGGiecj:JW5301.
eco:b1835.
PATRICi32118991. VBIEscCol129921_1913.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74905.2.
AP009048 Genomic DNA. Translation: BAA15648.2.
PIRiC64945.
RefSeqiNP_416349.2. NC_000913.3.
WP_001352260.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FRXX-ray2.90A/B/C/D1-479[»]
ProteinModelPortaliP76273.
SMRiP76273. Positions 7-474.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259158. 9 interactions.
STRINGi511145.b1835.

Proteomic databases

PaxDbiP76273.
PRIDEiP76273.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74905; AAC74905; b1835.
BAA15648; BAA15648; BAA15648.
GeneIDi946348.
KEGGiecj:JW5301.
eco:b1835.
PATRICi32118991. VBIEscCol129921_1913.

Organism-specific databases

EchoBASEiEB3777.
EcoGeneiEG14023. rsmF.

Phylogenomic databases

eggNOGiENOG4105CYJ. Bacteria.
COG0144. LUCA.
COG3270. LUCA.
HOGENOMiHOG000218115.
InParanoidiP76273.
KOiK11392.
OMAiWCAEGFW.
OrthoDBiEOG6091D0.
PhylomeDBiP76273.

Enzyme and pathway databases

BioCyciEcoCyc:G7008-MONOMER.
ECOL316407:JW5301-MONOMER.
MetaCyc:G7008-MONOMER.
BRENDAi2.1.1.178. 2026.

Miscellaneous databases

EvolutionaryTraceiP76273.
PROiP76273.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01579. 16SrRNA_methyltr_F.
InterProiIPR018314. Fmu/NOL1/Nop2p_CS.
IPR031341. Methyltr_RsmF_N.
IPR001678. MeTrfase_RsmB/NOP2.
IPR027391. Nol1_Nop2_Fmu_2.
IPR011023. Nop2p.
IPR023267. RCMT.
IPR023545. rRNA_ssu_MeTfrase_F.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
PF17125. Methyltr_RsmF_N. 1 hit.
PF13636. Methyltranf_PUA. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00446. nop2p. 1 hit.
PROSITEiPS01153. NOL1_NOP2_SUN. 1 hit.
PS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407."
    Moeller Andersen N., Douthwaite S.
    J. Mol. Biol. 359:777-786(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  5. "The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain."
    Hallberg B.M., Ericsson U.B., Johnson K.A., Moeller Andersen N., Douthwaite S., Nordlund P., Beuscher A.E. IV, Erlandsen H.
    J. Mol. Biol. 360:774-787(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS), CATALYTIC ACTIVITY.

Entry informationi

Entry nameiRSMF_ECOLI
AccessioniPrimary (citable) accession number: P76273
Secondary accession number(s): O07980
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: December 15, 1998
Last modified: May 11, 2016
This is version 121 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.