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Protein

Ribosomal RNA small subunit methyltransferase F

Gene

rsmF

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA.UniRule annotation

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei147S-adenosyl-L-methionineUniRule annotation1
Binding sitei174S-adenosyl-L-methionineUniRule annotation1
Binding sitei192S-adenosyl-L-methionineUniRule annotation1
Active sitei245NucleophileUniRule annotation1

GO - Molecular functioni

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 FUniRule annotation (EC:2.1.1.178UniRule annotation)
Alternative name(s):
16S rRNA m5C1407 methyltransferaseUniRule annotation
rRNA (cytosine-C(5)-)-methyltransferase RsmFUniRule annotation
Gene namesi
Name:rsmFUniRule annotation
Ordered Locus Names:VP1612
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000002493 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002850241 – 478Ribosomal RNA small subunit methyltransferase FAdd BLAST478

Interactioni

Protein-protein interaction databases

STRINGi223926.VP1612.

Structurei

3D structure databases

ProteinModelPortaliQ87PA5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni123 – 129S-adenosyl-L-methionine bindingUniRule annotation7

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CYJ. Bacteria.
COG0144. LUCA.
COG3270. LUCA.
HOGENOMiHOG000218115.
KOiK11392.
OMAiWCAEGFW.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01579. 16SrRNA_methyltr_F. 1 hit.
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.

Q87PA5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHPNVYIPDA FLEKIQTILP ANLNMEDFIS ACQRPLRKSI RVNTLKMSVE
60 70 80 90 100
DFVKRAEDKG WTLSPVPWCD NGFWIEADES VVPLGNTAEH MSGLFYIQEA
110 120 130 140 150
SSMMPVSALF MNDESYDAVL DTAAAPGSKT TQIAALMKNE GVLVANEYAA
160 170 180 190 200
SRVKVLHANI ERCGVRNAAL SNFDGRVFGG WLPEQFDAVL LDAPCSGEGT
210 220 230 240 250
VRKDEDAMKN WTQASVLEIA DTQKDLIESA FHALKPGGVL VYSTCTLSTE
260 270 280 290 300
ENQQVCHHLK ETFGDAVEFE SLDGLFENAN AALTEEGFLH IFPQVYDCEG
310 320 330 340 350
FFVARIRKHH SVEAPQVKKR MGKFPFVKAS KKESEEISKQ LHNALDIELP
360 370 380 390 400
SESTVWLRDK DVWLFPDALE PMIGELRFSR MGIKIAEAHK NGYRWQHQVA
410 420 430 440 450
TALATGAESN AIELTIEEAR EWYMGRDVRP QIIPEGLKTG KGEVLVKYQG
460 470
AIIGLGKWVS NRIKNGLPRE LVRDKNLF
Length:478
Mass (Da):53,449
Last modified:June 1, 2003 - v1
Checksum:i400919D74616CB28
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC59875.1.
RefSeqiNP_797991.1. NC_004603.1.
WP_005457106.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC59875; BAC59875; BAC59875.
GeneIDi1189119.
KEGGivpa:VP1612.
PATRICi20141400. VBIVibPar50997_1535.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC59875.1.
RefSeqiNP_797991.1. NC_004603.1.
WP_005457106.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87PA5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP1612.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC59875; BAC59875; BAC59875.
GeneIDi1189119.
KEGGivpa:VP1612.
PATRICi20141400. VBIVibPar50997_1535.

Phylogenomic databases

eggNOGiENOG4105CYJ. Bacteria.
COG0144. LUCA.
COG3270. LUCA.
HOGENOMiHOG000218115.
KOiK11392.
OMAiWCAEGFW.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01579. 16SrRNA_methyltr_F. 1 hit.
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...

Entry informationi

Entry nameiRSMF_VIBPA
AccessioniPrimary (citable) accession number: Q87PA5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: June 1, 2003
Last modified: November 2, 2016
This is version 84 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

Complete proteome, Reference proteome

Documents

  1. 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.