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Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Haemophilus influenzae (strain PittEE)
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 sitei110 – 1101Proton acceptorUniRule annotation
Metal bindingi130 – 1301Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi134 – 1341Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi137 – 1371Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Binding sitei216 – 2161S-adenosyl-L-methionineUniRule annotation
Binding sitei317 – 3171S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation
Active sitei360 – 3601S-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

BioCyciHINF374930:GJDD-223-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:CGSHiEE_01185
OrganismiHaemophilus influenzae (strain PittEE)
Taxonomic identifieri374930 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus

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 – 390390Dual-specificity RNA methyltransferase RlmNPRO_0000350203Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi123 ↔ 360(transient)UniRule annotation

Keywords - PTMi

Disulfide bond

Structurei

3D structure databases

ProteinModelPortaliA5UAC2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni184 – 1852S-adenosyl-L-methionine bindingUniRule annotation
Regioni238 – 2403S-adenosyl-L-methionine bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0820.
HOGENOMiHOG000217992.
KOiK06941.
OrthoDBiEOG6DJZ2N.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN.
InterProiIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
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.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00048. rRNA_mod_RlmN. 1 hit.

Sequencei

Sequence statusi: Complete.

A5UAC2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MCNNEAKMSE LLSVQSDAPA KKINLMDLTR QQMREFFKEL GEKPFRADQL
60 70 80 90 100
VKWIYHFGED NFDNMTNINK KLREKLKAVA EIKAPEVAVE QRSADGTIKW
110 120 130 140 150
AMQVGEQQVE TVYIPEADRA TLCVSSQVGC ALACTFCSTA QQGFNRNLTV
160 170 180 190 200
SEIIGQVWRA SKIIGNFGVT GVRPITNVVM MGMGEPLLNV ANVVPAMEIM
210 220 230 240 250
LDDFAYGLSK RRVTLSTSGV VPALDNLSKM IDVALAISLH APNDELRDEI
260 270 280 290 300
VPINKKYNIK TLIDSVNRYL TVSNANHGKV TIEYVMLDHV NDGVEHAHQL
310 320 330 340 350
ADVLKNTPCK INLIPWNPFP EAPYAKSSNT RIDRFQKTLM EYDFTVIIRK
360 370 380 390
TRGDDIDAAC GQLAGDVIDR TKRTAMKRQF GQNIGVTEVN
Length:390
Mass (Da):43,570
Last modified:September 2, 2008 - v2
Checksum:i85E174CE9CF12465
GO

Sequence cautioni

The sequence ABQ97723.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000671 Genomic DNA. Translation: ABQ97723.1. Different initiation.
RefSeqiWP_005662659.1. NC_009566.1.
YP_001290106.1. NC_009566.1.

Genome annotation databases

EnsemblBacteriaiABQ97723; ABQ97723; CGSHiEE_01185.
KEGGihip:CGSHiEE_01185.
PATRICi20276473. VBIHaeInf81350_0235.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000671 Genomic DNA. Translation: ABQ97723.1. Different initiation.
RefSeqiWP_005662659.1. NC_009566.1.
YP_001290106.1. NC_009566.1.

3D structure databases

ProteinModelPortaliA5UAC2.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ97723; ABQ97723; CGSHiEE_01185.
KEGGihip:CGSHiEE_01185.
PATRICi20276473. VBIHaeInf81350_0235.

Phylogenomic databases

eggNOGiCOG0820.
HOGENOMiHOG000217992.
KOiK06941.
OrthoDBiEOG6DJZ2N.

Enzyme and pathway databases

BioCyciHINF374930:GJDD-223-MONOMER.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN.
InterProiIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
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.
SMARTiSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00048. rRNA_mod_RlmN. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains."
    Hogg J.S., Hu F.Z., Janto B., Boissy R., Hayes J., Keefe R., Post J.C., Ehrlich G.D.
    Genome Biol. 8:R103.1-R103.18(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PittEE.

Entry informationi

Entry nameiRLMN_HAEIE
AccessioniPrimary (citable) accession number: A5UAC2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: September 2, 2008
Last modified: June 24, 2015
This is version 55 of the entry and version 2 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.