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Protein

Ribosomal RNA small subunit methyltransferase F

Gene

rsmF

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates the cytosines at positions 1400 (m5C1400), 1404 (m5C1404) and 1407 (m5C1407) of 16S rRNA. C1400, C1404 and C1407 are methylated in a 30S subunit substrate, but only C1400 and C1404 are methylated when naked 16S rRNA is the substrate. Methylation by RsmF may facilitate growth at temperatures outside the optimal growth temperature.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + cytosine(1400) in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(1400) in 16S rRNA.1 Publication
S-adenosyl-L-methionine + cytosine(1404) in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(1404) in 16S rRNA.1 Publication
S-adenosyl-L-methionine + cytosine(1407) in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(1407) in 16S rRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei133 – 1331S-adenosyl-L-methionine1 Publication
Binding sitei138 – 1381S-adenosyl-L-methionine1 Publication
Binding sitei177 – 1771S-adenosyl-L-methionine1 Publication
Active sitei230 – 2301NucleophilePROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

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

BioCyciTTHE300852:GH8R-1423-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA small subunit methyltransferase FBy similarity (EC:2.1.1.-1 Publication, EC:2.1.1.1781 Publication)
Alternative name(s):
rRNA (cytosine-C(5)-)-methyltransferase RsmFBy similarity
Gene namesi
Name:rsmF1 Publication
Ordered Locus Names:TTHA1387Imported
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 456456Ribosomal RNA small subunit methyltransferase FPRO_0000431481Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi300852.TTHA1387.

Structurei

Secondary structure

1
456
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1411Combined sources
Helixi15 – 173Combined sources
Helixi18 – 269Combined sources
Beta strandi33 – 364Combined sources
Turni38 – 403Combined sources
Helixi43 – 497Combined sources
Beta strandi55 – 573Combined sources
Beta strandi60 – 656Combined sources
Beta strandi73 – 753Combined sources
Helixi76 – 794Combined sources
Beta strandi82 – 854Combined sources
Helixi89 – 913Combined sources
Helixi92 – 976Combined sources
Beta strandi104 – 1096Combined sources
Helixi114 – 1229Combined sources
Turni123 – 1253Combined sources
Beta strandi127 – 1326Combined sources
Helixi136 – 14914Combined sources
Beta strandi154 – 1563Combined sources
Helixi160 – 1678Combined sources
Beta strandi171 – 1777Combined sources
Helixi183 – 1853Combined sources
Turni186 – 1883Combined sources
Helixi193 – 1953Combined sources
Helixi200 – 21617Combined sources
Beta strandi219 – 23012Combined sources
Helixi234 – 2363Combined sources
Helixi238 – 24710Combined sources
Beta strandi251 – 2544Combined sources
Beta strandi262 – 2643Combined sources
Helixi267 – 2693Combined sources
Turni270 – 2723Combined sources
Helixi274 – 2785Combined sources
Beta strandi279 – 2824Combined sources
Turni284 – 2863Combined sources
Beta strandi287 – 2904Combined sources
Beta strandi292 – 2998Combined sources
Helixi317 – 33014Combined sources
Beta strandi338 – 3414Combined sources
Beta strandi344 – 3474Combined sources
Beta strandi361 – 37111Combined sources
Beta strandi374 – 3785Combined sources
Helixi379 – 3846Combined sources
Turni386 – 3883Combined sources
Beta strandi393 – 3953Combined sources
Beta strandi397 – 4004Combined sources
Helixi405 – 4117Combined sources
Beta strandi423 – 43210Combined sources
Beta strandi435 – 44511Combined sources
Beta strandi448 – 4514Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3M6UX-ray1.40A/B1-456[»]
3M6VX-ray1.82A/B1-456[»]
3M6WX-ray1.30A1-456[»]
3M6XX-ray1.68A1-456[»]
ProteinModelPortaliQ5SII2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SII2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni109 – 1157S-adenosyl-L-methionine binding1 Publication

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB/NOP family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105CYJ. Bacteria.
COG0144. LUCA.
HOGENOMiHOG000218116.
OMAiHPFFYAG.
OrthoDBiEOG6091D0.
PhylomeDBiQ5SII2.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR031341. Methyltr_RsmF_N.
IPR001678. MeTrfase_RsmB/NOP2.
IPR023267. RCMT.
IPR031340. RsmF_methylt_CI.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
PF17125. Methyltr_RsmF_N. 1 hit.
PF17126. RsmF_methylt_CI. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5SII2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLPKAFLSRM AELLGEEFPA FLKALTEGKR TYGLRVNTLK LPPEAFQRIS
60 70 80 90 100
PWPLRPIPWC QEGFYYPEEA RPGPHPFFYA GLYYIQEPSA QAVGVLLDPK
110 120 130 140 150
PGERVLDLAA APGGKTTHLA ARMGGKGLLL ANEVDGKRVR GLLENVERWG
160 170 180 190 200
APLAVTQAPP RALAEAFGTY FHRVLLDAPC SGEGMFRKDR EAARHWGPSA
210 220 230 240 250
PKRMAEVQKA LLAQASRLLG PGGVLVYSTC TFAPEENEGV VAHFLKAHPE
260 270 280 290 300
FRLEDARLHP LFAPGVPEWG EGNPELLKTA RLWPHRLEGE GHFLARFRKE
310 320 330 340 350
GGAWSTPRLE RPSPLSQEAL RAFRGFLEEA GLTLEGPVLD RAGHLYLLPE
360 370 380 390 400
GLPTLLGLKA PAPGLYLGKV QKGRFLPARA LALAFGATLP WPEGLPRLAL
410 420 430 440 450
TPEDPRALAF ATGEGVAWEG EDHPLALVVL KTAAGEFPLD FGKAKRGVLR

PVGVGL
Length:456
Mass (Da):49,740
Last modified:December 21, 2004 - v1
Checksum:iC440940306A6683E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD71210.1.
RefSeqiWP_011228642.1. NC_006461.1.
YP_144653.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71210; BAD71210; BAD71210.
GeneIDi3168094.
KEGGittj:TTHA1387.
PATRICi23957735. VBITheThe93045_1363.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD71210.1.
RefSeqiWP_011228642.1. NC_006461.1.
YP_144653.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3M6UX-ray1.40A/B1-456[»]
3M6VX-ray1.82A/B1-456[»]
3M6WX-ray1.30A1-456[»]
3M6XX-ray1.68A1-456[»]
ProteinModelPortaliQ5SII2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA1387.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD71210; BAD71210; BAD71210.
GeneIDi3168094.
KEGGittj:TTHA1387.
PATRICi23957735. VBITheThe93045_1363.

Phylogenomic databases

eggNOGiENOG4105CYJ. Bacteria.
COG0144. LUCA.
HOGENOMiHOG000218116.
OMAiHPFFYAG.
OrthoDBiEOG6091D0.
PhylomeDBiQ5SII2.

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-1423-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ5SII2.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR031341. Methyltr_RsmF_N.
IPR001678. MeTrfase_RsmB/NOP2.
IPR023267. RCMT.
IPR031340. RsmF_methylt_CI.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF01189. Methyltr_RsmB-F. 1 hit.
PF17125. Methyltr_RsmF_N. 1 hit.
PF17126. RsmF_methylt_CI. 1 hit.
[Graphical view]
PRINTSiPR02008. RCMTFAMILY.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51686. SAM_MT_RSMB_NOP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  2. "Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus."
    Demirci H., Larsen L.H., Hansen T., Rasmussen A., Cadambi A., Gregory S.T., Kirpekar F., Jogl G.
    RNA 16:1584-1596(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY.
    Strain: HB8 / ATCC 27634 / DSM 579.

Entry informationi

Entry nameiRSMF_THET8
AccessioniPrimary (citable) accession number: Q5SII2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 7, 2015
Last sequence update: December 21, 2004
Last modified: May 11, 2016
This is version 68 of the entry and version 1 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.