Dual-specificity RNA methyltransferase RlmN - Stenotrophomonas maltophilia JV3

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G0JX73 (G0JX73_STEMA) Unreviewed, UniProtKB/TrEMBL

Last modified April 3, 2013. Version 13. History...

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

Third-party data

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

Names and origin

Protein names

Recommended name:
Dual-specificity RNA methyltransferase RlmN HAMAP-Rule MF_01849
EC=2.1.1.- HAMAP-Rule MF_01849
EC=2.1.1.192 HAMAP-Rule MF_01849

Alternative name(s):
23S rRNA (adenine(2503)-C(2))-methyltransferase HAMAP-Rule MF_01849
23S rRNA m2A2503 methyltransferase HAMAP-Rule MF_01849
Ribosomal RNA large subunit methyltransferase N HAMAP-Rule MF_01849
tRNA (adenine(37)-C(2))-methyltransferase HAMAP-Rule MF_01849
tRNA m2A37 methyltransferase HAMAP-Rule MF_01849

Gene names

Name:	rlmN HAMAP-Rule MF_01849
ORF Names:	BurJV3_1703 EMBL AEM51032.1

Organism

Stenotrophomonas maltophilia JV3 EMBL AEM51032.1

Taxonomic identifier

868597 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Xanthomonadales › Xanthomonadaceae › Stenotrophomonas › Stenotrophomonas maltophilia group ›

Protein attributes

Sequence length	401 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 SAAS SAAS004383 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. HAMAP-Rule MF_01849 SAAS SAAS004383
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_01849 SAAS SAAS004383.
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. HAMAP-Rule MF_01849

Ontologies

Keywords
Biological process	rRNA processing HAMAP-Rule MF_01849 SAAS SAAS004383 tRNA processing HAMAP-Rule MF_01849 SAAS SAAS004383
Cellular component	Cytoplasm HAMAP-Rule MF_01849 SAAS SAAS004383
Ligand	4Fe-4S HAMAP-Rule MF_01849 SAAS SAAS004383 Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine HAMAP-Rule MF_01849 SAAS SAAS004383
Molecular function	Methyltransferase HAMAP-Rule MF_01849 SAAS SAAS004383 EMBL AEM51032.1 Transferase
PTM	Disulfide bond HAMAP-Rule MF_01849 SAAS SAAS004383
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

Regions

Region

187 – 188

S-adenosyl-L-methionine binding By similarity HAMAP-Rule MF_01849

Region

241 – 243

S-adenosyl-L-methionine binding By similarity HAMAP-Rule MF_01849

Sites

Active site

114

Proton acceptor By similarity HAMAP-Rule MF_01849

Active site

370

S-methylcysteine intermediate By similarity HAMAP-Rule MF_01849

Metal binding

134

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849

Metal binding

138

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849

Metal binding

141

Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849

Binding site

219

S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01849

Binding site

327

S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen By similarity HAMAP-Rule MF_01849

Amino acid modifications

Disulfide bond

127 ↔ 370

(transient) By similarity HAMAP-Rule MF_01849

Sequences

Sequence

Length

Mass (Da)

Tools

G0JX73 [UniParc].

Last modified October 19, 2011. Version 1.
Checksum: B67057045B7405E9
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FASTA

401

44,633

        10         20         30         40         50         60 
MNEVVQSPAI QPLPKSAPTA GKQNLLDLDR AGLEKFFVEV LGEKKFRAHQ VMKWIHHRYV 

        70         80         90        100        110        120 
TDFDEMTDLG KVLRAKLQAH AEVLVPNIVF DKPSADGTHK WLLAMGVDGK NAIETVYIPD 

       130        140        150        160        170        180 
KTRGTLCVSS QVGCGLNCTF CSTATQGFNR NLTTAEIIGQ VWVAARHLGN VPHQMRRLTN 

       190        200        210        220        230        240 
VVMMGMGEPL MNFDNVVRAM SVMRDDLGYG LANKRVTLST SGLVPQIDRL SAESDVSLAV 

       250        260        270        280        290        300 
SLHAPNDALR ETLVPLNKKY PIAELMASCA RYLRANKRRE SVTFEYTLMK GINDKPEHAR 

       310        320        330        340        350        360 
ELARLMRQFD NAVQAKDSGK VNLIPFNPFP GTRYERSEEA HIRAFQKILL DSNVLTMVRR 

       370        380        390        400 
TRGDDIDAAC GQLKGQVMDR TRRQAEFNKT LQAGKGSDAA A

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References

[1]

"Complete sequence of Stenotrophomonas maltophilia JV3."
US DOE Joint Genome Institute
Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Ovchinnikova G., Teshima H., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Medau R.

Woyke T.
Submitted (AUG-2011) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: JV3 EMBL AEM51032.1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP002986 Genomic DNA. Translation: AEM51032.1.
RefSeq	YP_004792258.1. NC_015947.1.
3D structure databases
ProteinModelPortal	G0JX73.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AEM51032; AEM51032; BurJV3_1703.
GeneID	11046458.
KEGG	buj:BurJV3_1703.
Phylogenomic databases
KO	K06941.
Enzyme and pathway databases
BioCyc	SMAL868597:GHCG-1756-MONOMER.
Family and domain databases
Gene3D	3.20.20.70. 1 hit.
HAMAP	MF_01849. 23SrRNA_methyltr_N.
InterPro	IPR013785. Aldolase_TIM. IPR006638. Elp3/MiaB/NifB. IPR004383. rRNA_lsu_MTrfase_RlmN. IPR007197. rSAM. [Graphical view]
Pfam	PF04055. Radical_SAM. 1 hit. [Graphical view]
PIRSF	PIRSF006004. CHP00048. 1 hit.
SMART	SM00729. Elp3. 1 hit. [Graphical view]
TIGRFAMs	TIGR00048. TIGR00048. 1 hit.
ProtoNet	Search...

Entry information

Entry name

G0JX73_STEMA

Accession

Primary (citable) accession number: G0JX73

Entry history

Integrated into UniProtKB/TrEMBL:	October 19, 2011
Last sequence update:	October 19, 2011
Last modified:	April 3, 2013
This is version 13 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Regions

Sites

Amino acid modifications

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information