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B1XXL6

- RLMN_LEPCP

UniProt

B1XXL6 - RLMN_LEPCP

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Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
Status
Reviewed - 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 = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA.UniRule annotation
2 S-adenosyl-L-methionine + adenine(37) in tRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(37) in tRNA.UniRule annotation

Cofactori

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 sitei92 – 921Proton acceptorUniRule annotation
Metal bindingi112 – 1121Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi116 – 1161Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi119 – 1191Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Binding sitei211 – 2111S-adenosyl-L-methionineUniRule annotation
Binding sitei316 – 3161S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenUniRule annotation
Active sitei359 – 3591S-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

BioCyciLCHO395495:GHYL-2918-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Dual-specificity RNA methyltransferase RlmNUniRule annotation (EC:2.1.1.-UniRule 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:Lcho_2871
OrganismiLeptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6))
Taxonomic identifieri395495 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesLeptothrix
ProteomesiUP000001693: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 393393Dual-specificity RNA methyltransferase RlmNPRO_0000350237Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi105 ↔ 359(transient)UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi395495.Lcho_2871.

Structurei

3D structure databases

ProteinModelPortaliB1XXL6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni179 – 1802S-adenosyl-L-methionine bindingUniRule annotation
Regioni233 – 2353S-adenosyl-L-methionine bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0820.
HOGENOMiHOG000217992.
KOiK06941.
OMAiHEGSKFE.
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. TIGR00048. 1 hit.

Sequencei

Sequence statusi: Complete.

B1XXL6-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTAVNLLDFD LDALAAYCEQ LGEKRFRAVQ LFRWIHQRGA ADFGQMSDLA
60 70 80 90 100
KSLRSKLADV ACIAPLRVLS EHRSSDGTIK WLFDVGDGNA VETVYIPEDD
110 120 130 140 150
RATLCISSQA GCAVGCRFCS TGHQGFSRNL STAEILAQLW YAEHSLRRER
160 170 180 190 200
AEGVSVGARA ATGPASERII SNVVMMGMGE PLQNYAAVLP ALRVMLDDHG
210 220 230 240 250
YGLSRRRVTV STSGVVPMID RLAADLPVAL AVSLHACDDA LRDVLVPLNR
260 270 280 290 300
KYPLAELLGA CQAYLASAPR DFITFEYCML DGVNDSDEQA RALLKLVGDK
310 320 330 340 350
GPVGRLPCKF NLIPFNPFPE SGLKRSGNER VQAFAQVLID GGLVTTVRKT
360 370 380 390
RGDDIDAACG QLAGEVQDRT RVQERMTRSP IRVIRSAAQP DAA
Length:393
Mass (Da):42,738
Last modified:May 20, 2008 - v1
Checksum:i34A9397DB5B1FA23
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001013 Genomic DNA. Translation: ACB35136.1.
RefSeqiYP_001791901.1. NC_010524.1.

Genome annotation databases

EnsemblBacteriaiACB35136; ACB35136; Lcho_2871.
GeneIDi6159746.
KEGGilch:Lcho_2871.
PATRICi22396153. VBILepCho83238_2902.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001013 Genomic DNA. Translation: ACB35136.1 .
RefSeqi YP_001791901.1. NC_010524.1.

3D structure databases

ProteinModelPortali B1XXL6.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 395495.Lcho_2871.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACB35136 ; ACB35136 ; Lcho_2871 .
GeneIDi 6159746.
KEGGi lch:Lcho_2871.
PATRICi 22396153. VBILepCho83238_2902.

Phylogenomic databases

eggNOGi COG0820.
HOGENOMi HOG000217992.
KOi K06941.
OMAi HEGSKFE.
OrthoDBi EOG6DJZ2N.

Enzyme and pathway databases

BioCyci LCHO395495:GHYL-2918-MONOMER.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_01849. RNA_methyltr_RlmN.
InterProi IPR013785. Aldolase_TIM.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view ]
PANTHERi PTHR30544. PTHR30544. 1 hit.
Pfami PF04055. Radical_SAM. 1 hit.
[Graphical view ]
PIRSFi PIRSF006004. CHP00048. 1 hit.
TIGRFAMsi TIGR00048. TIGR00048. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51168 / LMG 8142 / SP-6.

Entry informationi

Entry nameiRLMN_LEPCP
AccessioniPrimary (citable) accession number: B1XXL6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: May 20, 2008
Last modified: October 29, 2014
This is version 46 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

External Data

Dasty 3