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Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)
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. m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity.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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei94 – 941Proton acceptorUniRule annotation
Metal bindingi114 – 1141Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi118 – 1181Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi121 – 1211Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Binding sitei191 – 1911S-adenosyl-L-methionineUniRule annotation
Binding sitei289 – 2891S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation
Active sitei332 – 3321S-methylcysteine intermediateUniRule annotation

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

Enzyme and pathway databases

BioCyciGMET269799:GHNY-2723-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
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:Gmet_2685
OrganismiGeobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)
Taxonomic identifieri269799 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfuromonadalesGeobacteraceaeGeobacter
Proteomesi
  • UP000007073 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 346346Dual-specificity RNA methyltransferase RlmNPRO_0000350194Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi107 ↔ 332(transient)UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi269799.Gmet_2685.

Structurei

3D structure databases

ProteinModelPortaliQ39S71.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni159 – 1602S-adenosyl-L-methionine bindingUniRule annotation
Regioni213 – 2153S-adenosyl-L-methionine bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C55. Bacteria.
COG0820. LUCA.
HOGENOMiHOG000217991.
KOiK06941.
OMAiIYHFGVS.
OrthoDBiEOG6DJZ2N.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN.
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.

Q39S71-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMNGKIDIKN LTLDDLIAFL AGKGKERYRA RQIFKWLYQK DARSFAEMTD
60 70 80 90 100
LAKDLRRDLE ETAVISDLEP EAMEVSRDGT RKYLFRLEDG NTVESVLIPE
110 120 130 140 150
EDRTTLCISS QVGCAMACEF CLTGTFRLTR NLTAGEIVNQ ICAVRRDVPV
160 170 180 190 200
RNIVFMGMGE PLANLDNVVK ALKIILHDDG LQFSTRRVTV STSGLVPEME
210 220 230 240 250
RLGREVTVNL AVSLNATTDE VRDRIMPVNR RYPLRLLLDA CRSYPLPGRR
260 270 280 290 300
KITIEYVMIK GLNDSLEDAK RLVKLLSDIS SKINLIPFNE HDGCSFKSPD
310 320 330 340
QGAIDVFHSY LLSKHFTVIT RSSRGSDISA ACGQLKGKLD KNVSGI
Length:346
Mass (Da):38,838
Last modified:November 22, 2005 - v1
Checksum:iDDBD5061246D9D2C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000148 Genomic DNA. Translation: ABB32903.1.
RefSeqiWP_004511775.1. NC_007517.1.

Genome annotation databases

EnsemblBacteriaiABB32903; ABB32903; Gmet_2685.
KEGGigme:Gmet_2685.
PATRICi22004618. VBIGeoMet55070_2722.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000148 Genomic DNA. Translation: ABB32903.1.
RefSeqiWP_004511775.1. NC_007517.1.

3D structure databases

ProteinModelPortaliQ39S71.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi269799.Gmet_2685.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB32903; ABB32903; Gmet_2685.
KEGGigme:Gmet_2685.
PATRICi22004618. VBIGeoMet55070_2722.

Phylogenomic databases

eggNOGiENOG4105C55. Bacteria.
COG0820. LUCA.
HOGENOMiHOG000217991.
KOiK06941.
OMAiIYHFGVS.
OrthoDBiEOG6DJZ2N.

Enzyme and pathway databases

BioCyciGMET269799:GHNY-2723-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN.
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...

Publicationsi

  1. "Complete sequence of Geobacter metallireducens GS-15."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Di Bartolo G., Chain P., Schmutz J., Larimer F., Land M., Kyrpides N., Ivanova N., Richardson P.
    Submitted (OCT-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: GS-15 / ATCC 53774 / DSM 7210.

Entry informationi

Entry nameiRLMN_GEOMG
AccessioniPrimary (citable) accession number: Q39S71
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: November 22, 2005
Last modified: May 11, 2016
This is version 73 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.