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D4HYC6 (D4HYC6_ERWAC) Unreviewed, UniProtKB/TrEMBL

Last modified May 29, 2013. Version 24. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended 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:yfgB EMBL CBA22015.1
Synonyms:rlmN HAMAP-Rule MF_01849
Ordered Locus Names:EAMY_2582 EMBL CBA22015.1
OrganismErwinia amylovora (strain CFBP1430) [Complete proteome] [HAMAP] EMBL CBA22015.1
Taxonomic identifier665029 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Erwinia ›

Protein attributes

Sequence length388 AA.
Sequence statusComplete.
Protein existenceInferred 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 SAAS SAAS004383

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.

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Region183 – 1842S-adenosyl-L-methionine binding By similarity HAMAP-Rule MF_01849
Region237 – 2393S-adenosyl-L-methionine binding By similarity HAMAP-Rule MF_01849

Sites

Active site1091Proton acceptor By similarity HAMAP-Rule MF_01849
Active site3591S-methylcysteine intermediate By similarity HAMAP-Rule MF_01849
Metal binding1291Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849
Metal binding1331Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849
Metal binding1361Iron-sulfur (4Fe-4S-S-AdoMet) By similarity HAMAP-Rule MF_01849
Binding site2151S-adenosyl-L-methionine By similarity HAMAP-Rule MF_01849
Binding site3161S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen By similarity HAMAP-Rule MF_01849

Amino acid modifications

Disulfide bond122 ↔ 359(transient) By similarity HAMAP-Rule MF_01849

Sequences

Sequence LengthMass (Da)Tools
D4HYC6 [UniParc].

Last modified May 18, 2010. Version 1.
Checksum: 5F8114AA5E3880EB

FASTA38843,121
        10         20         30         40         50         60 
MSELNVTPSS VSPAITPKKE KINLLDLNRQ QMREFFASLG EKPFRADQVM KWIYHYCCDD 

        70         80         90        100        110        120 
FNEMTDINKV FRNRLQELAE IRAPEVAEEQ RSADGTIKWA IQVGGQQVET VYIPEKDRAT 

       130        140        150        160        170        180 
LCVSSQVGCA LECKFCSTAQ QGFNRNLRVS EIIGQVWRAA KIIGAAKVTG QRPITNVVMM 

       190        200        210        220        230        240 
GMGEPLLNLT NVVPAMEIML DDFGFGLSKR RVTLSTSGVV PALDKLGDMI DVALAISLHA 

       250        260        270        280        290        300 
PNDTIRDEIV PINKKYNIET FLASVSRYIG KSNANQGRVT IEYVMLDHIN DSTDNAHELA 

       310        320        330        340        350        360 
ALLKDTPCKI NLIPWNPFPG APYGRSSNSR IDRFSKVLME YGFTTIVRKT RGDDIDAACG 

       370        380 
QLAGDVIDRT KRTLKKKMAG EAISVKAL

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References

[1]"Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp."
Smits T.H., Rezzonico F., Kamber T., Blom J., Goesmann A., Frey J.E., Duffy B.
Mol. Plant Microbe Interact. 23:384-393(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CFBP1430.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		FN434113 Genomic DNA. Translation: CBA22015.1.
RefSeqYP_003531937.1. NC_013961.1.

3D structure databases

ProteinModelPortalD4HYC6.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCBA22015; CBA22015; EAMY_2582.
GeneID8913592.
KEGGeam:EAMY_2582.
PATRIC35409230. VBIErwAmy142366_2488.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHOG000217992.
KOK06941.

Enzyme and pathway databases

BioCycEAMY665029:GCM3-2640-MONOMER.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_01849. RNA_methyltr_RlmN.
InterProIPR013785. Aldolase_TIM.
IPR006638. Elp3/MiaB/NifB.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
[Graphical view]
PANTHERPTHR30544. PTHR30544. 1 hit.
PfamPF04055. Radical_SAM. 1 hit.
[Graphical view]
PIRSFPIRSF006004. CHP00048. 1 hit.
SMARTSM00729. Elp3. 1 hit.
[Graphical view]
TIGRFAMsTIGR00048. TIGR00048. 1 hit.
ProtoNetSearch...

Entry information

Entry nameD4HYC6_ERWAC
AccessionPrimary (citable) accession number: D4HYC6
Entry history
Integrated into UniProtKB/TrEMBL: May 18, 2010
Last sequence update: May 18, 2010
Last modified: May 29, 2013
This is version 24 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info