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Protein

Dual-specificity RNA methyltransferase RlmN

Gene

rlmN

Organism
Coxiella burnetii (strain RSA 493 / Nine Mile phase I)
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. 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.

Miscellaneous

Reaction proceeds by a ping-pong mechanism involving intermediate methylation of a conserved cysteine residue.

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.
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.

Cofactori

[4Fe-4S] clusterNote: Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei93Proton acceptor1
Metal bindingi113Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi117Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi120Iron-sulfur (4Fe-4S-S-AdoMet)1
Binding sitei194S-adenosyl-L-methionine1
Binding sitei293S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen1
Active sitei336S-methylcysteine intermediate1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionMethyltransferase, Transferase
Biological processrRNA processing, tRNA processing
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Names & Taxonomyi

Protein namesi
Recommended name:
Dual-specificity RNA methyltransferase RlmN (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 namesi
Name:rlmN
Ordered Locus Names:CBU_1252
OrganismiCoxiella burnetii (strain RSA 493 / Nine Mile phase I)
Taxonomic identifieri227377 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaLegionellalesCoxiellaceaeCoxiella
Proteomesi
  • UP000002671 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003501391 – 370Dual-specificity RNA methyltransferase RlmNAdd BLAST370

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi106 ↔ 336(transient)

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi227377.CBU_1252.

Structurei

3D structure databases

ProteinModelPortaliQ83C77.
SMRiQ83C77.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni162 – 163S-adenosyl-L-methionine binding2
Regioni216 – 218S-adenosyl-L-methionine binding3

Sequence similaritiesi

Belongs to the radical SAM superfamily. RlmN family.

Phylogenomic databases

eggNOGiENOG4105C55. Bacteria.
COG0820. LUCA.
HOGENOMiHOG000217992.
KOiK06941.
OMAiCGQLANK.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_01849. RNA_methyltr_RlmN. 1 hit.
InterProiView protein in InterPro
IPR013785. Aldolase_TIM.
IPR027492. RNA_MTrfase_RlmN.
IPR004383. rRNA_lsu_MTrfase_RlmN/Cfr.
IPR007197. rSAM.
PANTHERiPTHR30544. PTHR30544. 1 hit.
PfamiView protein in Pfam
PF04055. Radical_SAM. 1 hit.
PIRSFiPIRSF006004. CHP00048. 1 hit.
SFLDiSFLDF00275. adenosine_C2_methyltransferase. 1 hit.
SFLDS00029. Radical_SAM. 1 hit.
TIGRFAMsiTIGR00048. rRNA_mod_RlmN. 1 hit.

Sequencei

Sequence statusi: Complete.

Q83C77-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTEKINLLNL SEPELQGFIA SQGQPLYRAT QLLQWIHQRG VTDFSLMTDL
60 70 80 90 100
SKPFRQQLSE ASFVRVPELA LERVSADGTH KWLFRLADNN KIETVFIPDR
110 120 130 140 150
KRGTLCVSSQ VGCALNCSFC ATGKEGFNRN LTLAEIIGQV WLAARLLKSP
160 170 180 190 200
YKITNVVMMG MGEPLLNYEA VVAAMHLMMH DHAYGLSKYR VTLSTSGVIP
210 220 230 240 250
AMRRLREESP VSLAVSLHAP NDALRNVLIP LNKKYSLDQL IPLCRDYYSR
260 270 280 290 300
GSKRCVTFEY VMIEGMNDRL IDAKQLIRLL ADVPCKINLI PFNSFQGTAY
310 320 330 340 350
RCSTESAISV FQKCLMDAGF NTRVRRTRGD DIAGACGQLA GQFHDRTGRH
360 370
QRWVQKQGHD FNRPIPAIDH
Length:370
Mass (Da):41,733
Last modified:June 1, 2003 - v1
Checksum:i0558478862C5536C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016828 Genomic DNA. Translation: AAO90760.1.
RefSeqiNP_820246.1. NC_002971.3.
WP_010958104.1. NC_002971.4.

Genome annotation databases

EnsemblBacteriaiAAO90760; AAO90760; CBU_1252.
GeneIDi1209157.
31483951.
KEGGicbu:CBU_1252.
PATRICifig|227377.7.peg.1243.

Similar proteinsi

Entry informationi

Entry nameiRLMN_COXBU
AccessioniPrimary (citable) accession number: Q83C77
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: June 1, 2003
Last modified: October 25, 2017
This is version 98 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Coxiella burnetii
    Coxiella burnetii (strain RSA 493): entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families