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Protein

Probable dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Frankia sp. (strain CcI3)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Specifically methylates position 2 of adenine 2503 in 23S rRNA and position 2 of adenine 37 in tRNAs.UniRule annotation

Catalytic activityi

2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin.UniRule annotation
2 S-adenosyl-L-methionine + adenine(37) in tRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(37) in tRNA + 2 oxidized [2Fe-2S] ferredoxin.UniRule annotation

Cofactori

[4Fe-4S] clusterUniRule annotationNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei127Proton acceptorUniRule annotation1
Metal bindingi147Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation1
Metal bindingi151Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation1
Metal bindingi154Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation1
Binding sitei236S-adenosyl-L-methionineUniRule annotation1
Binding sitei335S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation1
Active sitei378S-methylcysteine intermediateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing, tRNA processing

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Names & Taxonomyi

Protein namesi
Recommended name:
Probable dual-specificity RNA methyltransferase RlmNUniRule annotation (EC:2.1.1.192UniRule annotation)
Alternative name(s):
23S rRNA (adenine(2503)-C(2))-methyltransferaseUniRule annotation
23S rRNA m2A2503 methyltransferaseUniRule annotation
Ribosomal RNA large subunit methyltransferase NUniRule annotation
tRNA (adenine(37)-C(2))-methyltransferaseUniRule annotation
tRNA m2A37 methyltransferaseUniRule annotation
Gene namesi
Name:rlmNUniRule annotation
Ordered Locus Names:Francci3_3577
OrganismiFrankia sp. (strain CcI3)
Taxonomic identifieri106370 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaFrankialesFrankiaceaeFrankia
Proteomesi
  • UP000001937 Componenti: Chromosome

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_00003501891 – 421Probable dual-specificity RNA methyltransferase RlmNAdd BLAST421

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi140 ↔ 378(transient)UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi106370.Francci3_3577.

Structurei

3D structure databases

ProteinModelPortaliQ2J713.
SMRiQ2J713.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni202 – 203S-adenosyl-L-methionine bindingUniRule annotation2
Regioni259 – 261S-adenosyl-L-methionine bindingUniRule annotation3

Sequence similaritiesi

Belongs to the radical SAM superfamily. RlmN family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C55. Bacteria.
COG0820. LUCA.
HOGENOMiHOG000217991.
KOiK06941.
OMAiFPLEKLM.
OrthoDBiPOG091H02LT.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view]
PANTHERiPTHR30544. PTHR30544. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF006004. CHP00048. 1 hit.
TIGRFAMsiTIGR00048. rRNA_mod_RlmN. 1 hit.

Sequencei

Sequence statusi: Complete.

Q2J713-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTATTAESGR PDQPPTAEAG RPVRLTLTRR AGRAPRHLAD LTRQERRDVA
60 70 80 90 100
VSLGQPAFRA DQVARHYYAR LIAADEPEAM TDLPERDRQP LLDALLPRLL
110 120 130 140 150
VPVRTLSCDD GLTRKTAWRT VDGASLESVI MRYPDRATVC VSSQAGCGMG
160 170 180 190 200
CPFCATGQGG LTRNLSTAEI VEQVVHAARV LRRRELAGGE TRLSNVVFMG
210 220 230 240 250
MGEPLANYAA VIAALRRLTA HPPEGLGLSA RGLTVSTVGL VPAIRRLAGE
260 270 280 290 300
GLPVTLAVSL HAPDDVLRNE LVPINTRWPV VEVLAAAWEY AEVTGRRVSV
310 320 330 340 350
EYALIDGVND DVGRADALAD LLVGRLAHVN LIPLNPTGGS SWRASAPAGQ
360 370 380 390 400
RAFVRRLRDR GIVTTVRDTR GREIAAACGQ LAAEPAGKPE RTDRPEQVGS
410 420
DRLVEFGAVG STTPDGDRVL R
Length:421
Mass (Da):45,196
Last modified:March 7, 2006 - v1
Checksum:i9CEE0102341EFD7D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000249 Genomic DNA. Translation: ABD12929.1.
RefSeqiWP_011437953.1. NC_007777.1.

Genome annotation databases

EnsemblBacteriaiABD12929; ABD12929; Francci3_3577.
KEGGifra:Francci3_3577.
PATRICi21930582. VBIFraSp10456_3901.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000249 Genomic DNA. Translation: ABD12929.1.
RefSeqiWP_011437953.1. NC_007777.1.

3D structure databases

ProteinModelPortaliQ2J713.
SMRiQ2J713.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi106370.Francci3_3577.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD12929; ABD12929; Francci3_3577.
KEGGifra:Francci3_3577.
PATRICi21930582. VBIFraSp10456_3901.

Phylogenomic databases

eggNOGiENOG4105C55. Bacteria.
COG0820. LUCA.
HOGENOMiHOG000217991.
KOiK06941.
OMAiFPLEKLM.
OrthoDBiPOG091H02LT.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view]
PANTHERiPTHR30544. PTHR30544. 1 hit.
PfamiPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFiPIRSF006004. CHP00048. 1 hit.
TIGRFAMsiTIGR00048. rRNA_mod_RlmN. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRLMN_FRASC
AccessioniPrimary (citable) accession number: Q2J713
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: March 7, 2006
Last modified: November 2, 2016
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.UniRule annotation

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.