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Protein

Probable dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Streptococcus suis (strain 98HAH33)
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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei91 – 911Proton acceptorUniRule annotation
Metal bindingi111 – 1111Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi115 – 1151Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi118 – 1181Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Binding sitei195 – 1951S-adenosyl-L-methionineUniRule annotation
Binding sitei296 – 2961S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation
Active sitei340 – 3401S-methylcysteine intermediateUniRule annotation

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
  2. metal ion binding Source: UniProtKB-KW
  3. rRNA (adenine-C2-)-methyltransferase activity Source: UniProtKB-HAMAP
  4. rRNA binding Source: UniProtKB-HAMAP
  5. tRNA (adenine-C2-)-methyltransferase activity Source: UniProtKB-HAMAP
  6. tRNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. rRNA base methylation Source: UniProtKB-HAMAP
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

BioCyciSSUI391296:GI2E-1742-MONOMER.

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:SSU98_1686
OrganismiStreptococcus suis (strain 98HAH33)
Taxonomic identifieri391296 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
ProteomesiUP000000244: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 370370Probable dual-specificity RNA methyltransferase RlmNPRO_0000350469Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi104 ↔ 340(transient)UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi391296.SSU98_1686.

Structurei

3D structure databases

ProteinModelPortaliA4W3A5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni163 – 1642S-adenosyl-L-methionine bindingUniRule annotation
Regioni218 – 2203S-adenosyl-L-methionine bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0820.
HOGENOMiHOG000217991.
KOiK06941.
OMAiKEDNNLP.
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. TIGR00048. 1 hit.

Sequencei

Sequence statusi: Complete.

A4W3A5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKPSIYAFSQ ANLVDWILEN GEKKFRATQI WEWLYRSRVQ SFAEMTNLPK
60 70 80 90 100
SLIEKLEEHF VVNPLKQRIV QESKDGTIKY LFELPDGMLI ETVLMHQHYG
110 120 130 140 150
LSVCVTTQVG CNIGCTFCAS GLIPKQRDLT SGEIVAQIML VQKYLDERNQ
160 170 180 190 200
NERVSHIVVM GIGEPLDNYD NVMTFLRVVN DDKGLAIGAR HITVSTSGLA
210 220 230 240 250
PKIREFAREG VQVNLAVSLH APNNDLRSSI MRINRKFPIE VLFEAIEDYI
260 270 280 290 300
KVTNRRVTFE YIMLNEVNDG VEQAQELADL TKNIRKLSYI NLIPYNPVSE
310 320 330 340 350
HDQYSRSTKE RTLAFFDVLK KNGVNCVVRQ EHGTDIDAAC GQLRSNTLKK
360 370
DREKARARIA AAKAKAGIRA
Length:370
Mass (Da):42,060
Last modified:May 29, 2007 - v1
Checksum:iE90BAF008866B358
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000408 Genomic DNA. Translation: ABP92844.1.
RefSeqiYP_001201244.1. NC_009443.1.

Genome annotation databases

EnsemblBacteriaiABP92844; ABP92844; SSU98_1686.
GeneIDi5103113.
KEGGissv:SSU98_1686.
PATRICi19779594. VBIStrSui72275_1654.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000408 Genomic DNA. Translation: ABP92844.1.
RefSeqiYP_001201244.1. NC_009443.1.

3D structure databases

ProteinModelPortaliA4W3A5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi391296.SSU98_1686.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP92844; ABP92844; SSU98_1686.
GeneIDi5103113.
KEGGissv:SSU98_1686.
PATRICi19779594. VBIStrSui72275_1654.

Phylogenomic databases

eggNOGiCOG0820.
HOGENOMiHOG000217991.
KOiK06941.
OMAiKEDNNLP.
OrthoDBiEOG6DJZ2N.

Enzyme and pathway databases

BioCyciSSUI391296:GI2E-1742-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. TIGR00048. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates."
    Chen C., Tang J., Dong W., Wang C., Feng Y., Wang J., Zheng F., Pan X., Liu D., Li M., Song Y., Zhu X., Sun H., Feng T., Guo Z., Ju A., Ge J., Dong Y.
    , Sun W., Jiang Y., Wang J., Yan J., Yang H., Wang X., Gao G.F., Yang R., Wang J., Yu J.
    PLoS ONE 2:E315-E315(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 98HAH33.

Entry informationi

Entry nameiRLMN_STRS2
AccessioniPrimary (citable) accession number: A4W3A5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: May 29, 2007
Last modified: March 4, 2015
This is version 59 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

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.