Dual-specificity RNA methyltransferase RlmN - Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6)

Contribute

Send feedback

Read comments (?) or add your own

B1XXL6 (RLMN_LEPCP) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 39. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Dual-specificity RNA methyltransferase RlmN
EC=2.1.1.-
EC=2.1.1.192

Alternative name(s):
23S rRNA (adenine(2503)-C(2))-methyltransferase
23S rRNA m2A2503 methyltransferase
Ribosomal RNA large subunit methyltransferase N
tRNA (adenine(37)-C(2))-methyltransferase
tRNA m2A37 methyltransferase

Gene names

Name:	rlmN
Ordered Locus Names:	Lcho_2871

Organism

Leptothrix cholodnii (strain ATCC 51168 / LMG 8142 / SP-6) (Leptothrix discophora (strain SP-6)) [Complete proteome] [HAMAP]

Taxonomic identifier

395495 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Betaproteobacteria › Burkholderiales › Leptothrix ›

Protein attributes

Sequence length	393 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	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 By similarity. HAMAP-Rule MF_01849
Catalytic activity	2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA. HAMAP-Rule MF_01849 2 S-adenosyl-L-methionine + adenine₃₇ in tRNA = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine₃₇ in tRNA. HAMAP-Rule MF_01849
Cofactor	Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine By similarity.
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01849.
Miscellaneous	Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue By similarity. HAMAP-Rule MF_01849
Sequence similarities	Belongs to the radical SAM superfamily. RlmN family.

Ontologies

Keywords
Biological process	rRNA processing tRNA processing
Cellular component	Cytoplasm
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
PTM	Disulfide bond
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	rRNA base methylation Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW rRNA (adenine-C2-)-methyltransferase activity Inferred from electronic annotation. Source: HAMAP rRNA binding Inferred from electronic annotation. Source: HAMAP tRNA (adenine-C2-)-methyltransferase activity Inferred from electronic annotation. Source: HAMAP tRNA binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 393

393

Dual-specificity RNA methyltransferase RlmN HAMAP-Rule MF_01849

PRO_0000350237

Regions

Region

179 – 180

S-adenosyl-L-methionine binding By similarity

Region

233 – 235

S-adenosyl-L-methionine binding By similarity

Sites

Active site

Proton acceptor Potential

Active site

359

S-methylcysteine intermediate By similarity

Metal binding

112

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity

Metal binding

116

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity

Metal binding

119

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity

Binding site

211

S-adenosyl-L-methionine By similarity

Binding site

316

S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen By similarity

Amino acid modifications

Disulfide bond

105 ↔ 359

(transient) By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

B1XXL6 [UniParc].

Last modified May 20, 2008. Version 1.
Checksum: 34A9397DB5B1FA23
Show »

FASTA

393

42,738

        10         20         30         40         50         60 
MTAVNLLDFD LDALAAYCEQ LGEKRFRAVQ LFRWIHQRGA ADFGQMSDLA KSLRSKLADV 

        70         80         90        100        110        120 
ACIAPLRVLS EHRSSDGTIK WLFDVGDGNA VETVYIPEDD RATLCISSQA GCAVGCRFCS 

       130        140        150        160        170        180 
TGHQGFSRNL STAEILAQLW YAEHSLRRER AEGVSVGARA ATGPASERII SNVVMMGMGE 

       190        200        210        220        230        240 
PLQNYAAVLP ALRVMLDDHG YGLSRRRVTV STSGVVPMID RLAADLPVAL AVSLHACDDA 

       250        260        270        280        290        300 
LRDVLVPLNR KYPLAELLGA CQAYLASAPR DFITFEYCML DGVNDSDEQA RALLKLVGDK 

       310        320        330        340        350        360 
GPVGRLPCKF NLIPFNPFPE SGLKRSGNER VQAFAQVLID GGLVTTVRKT RGDDIDAACG 

       370        380        390 
QLAGEVQDRT RVQERMTRSP IRVIRSAAQP DAA

« Hide

References

[1]

"Complete sequence of Leptothrix cholodnii SP-6."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.

Richardson P.
Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 51168 / LMG 8142 / SP-6.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001013 Genomic DNA. Translation: ACB35136.1.
RefSeq	YP_001791901.1. NC_010524.1.
3D structure databases
ProteinModelPortal	B1XXL6.
ModBase	Search...
Protein-protein interaction databases
STRING	395495.Lcho_2871.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACB35136; ACB35136; Lcho_2871.
GeneID	6159746.
KEGG	lch:Lcho_2871.
PATRIC	22396153. VBILepCho83238_2902.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0820.
HOGENOM	HOG000217992.
KO	K06941.
OMA	IYHFGVS.
ProtClustDB	CLSK951482.
Enzyme and pathway databases
BioCyc	LCHO395495:GHYL-2918-MONOMER.
Family and domain databases
Gene3D	3.20.20.70. 1 hit.
HAMAP	MF_01849. RNA_methyltr_RlmN.
InterPro	IPR013785. Aldolase_TIM. IPR004383. rRNA_lsu_MTrfase_RlmN. IPR007197. rSAM. [Graphical view]
Pfam	PF04055. Radical_SAM. 1 hit. [Graphical view]
PIRSF	PIRSF006004. CHP00048. 1 hit.
TIGRFAMs	TIGR00048. TIGR00048. 1 hit.
ProtoNet	Search...

Entry information

Entry name

RLMN_LEPCP

Accession

Primary (citable) accession number: B1XXL6

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 2, 2008
Last sequence update:	May 20, 2008
Last modified:	May 1, 2013
This is version 39 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents