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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)DescriptionActionsGraphical viewLength
Binding sitei133S-adenosyl-L-methionine1 Publication1
Binding sitei138S-adenosyl-L-methionine1 Publication1
Binding sitei177S-adenosyl-L-methionine1 Publication1
Active sitei230NucleophilePROSITE-ProRule annotation1

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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00004314811 – 456Ribosomal RNA small subunit methyltransferase FAdd BLAST456

Interactioni

Protein-protein interaction databases

STRINGi300852.TTHA1387.

Structurei

Secondary structure

1456
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 14Combined sources11
Helixi15 – 17Combined sources3
Helixi18 – 26Combined sources9
Beta strandi33 – 36Combined sources4
Turni38 – 40Combined sources3
Helixi43 – 49Combined sources7
Beta strandi55 – 57Combined sources3
Beta strandi60 – 65Combined sources6
Beta strandi73 – 75Combined sources3
Helixi76 – 79Combined sources4
Beta strandi82 – 85Combined sources4
Helixi89 – 91Combined sources3
Helixi92 – 97Combined sources6
Beta strandi104 – 109Combined sources6
Helixi114 – 122Combined sources9
Turni123 – 125Combined sources3
Beta strandi127 – 132Combined sources6
Helixi136 – 149Combined sources14
Beta strandi154 – 156Combined sources3
Helixi160 – 167Combined sources8
Beta strandi171 – 177Combined sources7
Helixi183 – 185Combined sources3
Turni186 – 188Combined sources3
Helixi193 – 195Combined sources3
Helixi200 – 216Combined sources17
Beta strandi219 – 230Combined sources12
Helixi234 – 236Combined sources3
Helixi238 – 247Combined sources10
Beta strandi251 – 254Combined sources4
Beta strandi262 – 264Combined sources3
Helixi267 – 269Combined sources3
Turni270 – 272Combined sources3
Helixi274 – 278Combined sources5
Beta strandi279 – 282Combined sources4
Turni284 – 286Combined sources3
Beta strandi287 – 290Combined sources4
Beta strandi292 – 299Combined sources8
Helixi317 – 330Combined sources14
Beta strandi338 – 341Combined sources4
Beta strandi344 – 347Combined sources4
Beta strandi361 – 371Combined sources11
Beta strandi374 – 378Combined sources5
Helixi379 – 384Combined sources6
Turni386 – 388Combined sources3
Beta strandi393 – 395Combined sources3
Beta strandi397 – 400Combined sources4
Helixi405 – 411Combined sources7
Beta strandi423 – 432Combined sources10
Beta strandi435 – 445Combined sources11
Beta strandi448 – 451Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3M6UX-ray1.40A/B1-456[»]
3M6VX-ray1.82A/B1-456[»]
3M6WX-ray1.30A1-456[»]
3M6XX-ray1.68A1-456[»]
ProteinModelPortaliQ5SII2.
SMRiQ5SII2.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SII2.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni109 – 115S-adenosyl-L-methionine binding1 Publication7

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.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3M6UX-ray1.40A/B1-456[»]
3M6VX-ray1.82A/B1-456[»]
3M6WX-ray1.30A1-456[»]
3M6XX-ray1.68A1-456[»]
ProteinModelPortaliQ5SII2.
SMRiQ5SII2.
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.
PhylomeDBiQ5SII2.

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...

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: November 2, 2016
This is version 70 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.