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Protein

Ribosomal RNA large subunit methyltransferase J

Gene

rlmJ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Specifically methylates the adenine in position 2030 of 23S rRNA. Nascent 23S rRNA seems to be the natural substrate. Appears to be not necessary for ribosome assembly. Required for the utilization of extracellular DNA as the sole source of carbon and energy (PubMed:11591672, PubMed:16707682).UniRule annotation4 Publications

Miscellaneous

Recombinant protein prefers protein-free 23S rRNA to ribonucleoprotein particles containing only part of the 50S subunit proteins and does not methylate the assembled 50S subunit (PubMed:22847818). Recognizes a minimal substrate corresponding to helix 72; this shows that RlmJ requires only a small hairpin for activity and this suggests that RlmJ can methylate A2030 before the 23S RNA is completely transcribed, processed and folded (PubMed:23945937). Cannot modify single-stranded DNA having the same sequence as H72 (PubMed:23945937).2 Publications

Catalytic activityi

S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + N6-methyladenine(2030) in 23S rRNA.UniRule annotation2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei19S-adenosyl-L-methionine1 Publication1
Binding sitei42S-adenosyl-L-methionine; via carbonyl oxygen1 Publication1
Binding sitei100S-adenosyl-L-methionine1 Publication1
Binding sitei118S-adenosyl-L-methionine1 Publication1
Active sitei164Proton acceptor1 Publication1
Binding sitei164S-adenosyl-L-methionine1 Publication1

GO - Molecular functioni

  • 23S rRNA (adenine(2030)-N(6))-methyltransferase activity Source: EcoCyc
  • RNA binding Source: UniProtKB-KW
  • rRNA (adenine-N6-)-methyltransferase activity Source: UniProtKB

GO - Biological processi

  • carbon utilization Source: EcoCyc
  • rRNA base methylation Source: UniProtKB

Keywordsi

Molecular functionMethyltransferase, RNA-binding, Transferase
Biological processrRNA processing
LigandS-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG12234-MONOMER
MetaCyc:EG12234-MONOMER
BRENDAi2.1.1.266 2026

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA large subunit methyltransferase JUniRule annotation (EC:2.1.1.266UniRule annotation)
Alternative name(s):
23S rRNA (adenine(2030)-N6)-methyltransferaseUniRule annotation
23S rRNA m6A2030 methyltransferaseUniRule annotation
Gene namesi
Name:rlmJUniRule annotation
Synonyms:yhiR
Ordered Locus Names:b3499, JW3466
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12234 rlmJ

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

Pathology & Biotechi

Disruption phenotypei

The inactivation of the this gene results in the complete loss of A2030 modification, but does not cause the accumulation of ribosome assembly intermediates. The phenotype of rlmJ knockout gene is very mild under various growth conditions and at the stationary phase, except for a small growth advantage in anaerobic conditions. Only minor changes in the total E.coli proteome can be observed in a cell devoid of the 23S rRNA nucleotide A2030 methylation (PubMed:22847818). Mutants show a stationary-phase competition defect during coculture with wild-type cells (PubMed:11591672). Cells lacking this gene are unable to grow using DNA as a sole nutrition source, but have no defects in DNA uptake by electroporation or when made chemically competent (PubMed:11591672, PubMed:16707682).3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi4Y → A: Loss of catalytic activity. 1 Publication1
Mutagenesisi4Y → F: 40-fold reduction in catalytic activity. 1 Publication1
Mutagenesisi6H → D: Loss of catalytic activity. 1 Publication1
Mutagenesisi18K → A: Loss of catalytic activity. 1 Publication1
Mutagenesisi18K → R: 10-fold reduction in catalytic activity. 1 Publication1
Mutagenesisi164D → A: Loss of catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001695671 – 280Ribosomal RNA large subunit methyltransferase JAdd BLAST280

Proteomic databases

PaxDbiP37634
PRIDEiP37634

Interactioni

Subunit structurei

Monomer.UniRule annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei4Interaction with substrate rRNACurated1

Binary interactionsi

WithEntry#Exp.IntActNotes
yihIP0A8H62EBI-548165,EBI-552497

Protein-protein interaction databases

BioGridi4262505, 18 interactors
DIPiDIP-12371N
IntActiP37634, 20 interactors
STRINGi316385.ECDH10B_3675

Structurei

Secondary structure

1280
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 8Combined sources3
Turni9 – 11Combined sources3
Helixi13 – 29Combined sources17
Beta strandi32 – 34Combined sources3
Beta strandi37 – 42Combined sources6
Beta strandi45 – 49Combined sources5
Beta strandi53 – 56Combined sources4
Helixi60 – 63Combined sources4
Helixi65 – 67Combined sources3
Turni68 – 70Combined sources3
Helixi76 – 78Combined sources3
Helixi79 – 87Combined sources9
Turni88 – 91Combined sources4
Beta strandi96 – 98Combined sources3
Helixi100 – 107Combined sources8
Beta strandi113 – 117Combined sources5
Helixi123 – 130Combined sources8
Turni131 – 133Combined sources3
Beta strandi137 – 140Combined sources4
Turni144 – 146Combined sources3
Helixi147 – 150Combined sources4
Beta strandi159 – 163Combined sources5
Helixi170 – 186Combined sources17
Beta strandi190 – 200Combined sources11
Helixi201 – 213Combined sources13
Beta strandi219 – 227Combined sources9
Beta strandi231 – 234Combined sources4
Beta strandi237 – 244Combined sources8
Helixi249 – 264Combined sources16
Beta strandi270 – 278Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4BLUX-ray1.85A/B1-280[»]
4BLVX-ray2.00A/B1-280[»]
4BLWX-ray1.95A/B1-280[»]
ProteinModelPortaliP37634
SMRiP37634
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni143 – 144S-adenosyl-L-methionine binding1 Publication2

Sequence similaritiesi

Belongs to the RlmJ family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105D6S Bacteria
COG2961 LUCA
HOGENOMiHOG000262479
InParanoidiP37634
KOiK07115
OMAiTYAIWYP
PhylomeDBiP37634

Family and domain databases

HAMAPiMF_00934 23SrRNA_methyltr_J, 1 hit
InterProiView protein in InterPro
IPR002052 DNA_methylase_N6_adenine_CS
IPR007473 RlmJ
IPR029063 SAM-dependent_MTases
PANTHERiPTHR37426 PTHR37426, 1 hit
PfamiView protein in Pfam
PF04378 RsmJ, 1 hit
SUPFAMiSSF53335 SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS00092 N6_MTASE, 2 hits

Sequencei

Sequence statusi: Complete.

P37634-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLSYRHSFHA GNHADVLKHT VQSLIIESLK EKDKPFLYLD THAGAGRYQL
60 70 80 90 100
GSEHAERTGE YLEGIARIWQ QDDLPAELEA YINVVKHFNR SGQLRYYPGS
110 120 130 140 150
PLIARLLLRE QDSLQLTELH PSDYPLLRSE FQKDSRARVE KADGFQQLKA
160 170 180 190 200
KLPPVSRRGL ILIDPPYEMK TDYQAVVSGI AEGYKRFATG IYALWYPVVL
210 220 230 240 250
RQQIKRMIHD LEATGIRKIL QIELAVLPDS DRRGMTASGM IVINPPWKLE
260 270 280
QQMNNVLPWL HSKLVPAGTG HATVSWIVPE
Length:280
Mass (Da):31,942
Last modified:October 1, 1994 - v1
Checksum:i13B039C77C5B77A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00039 Genomic DNA Translation: AAB18475.1
U00096 Genomic DNA Translation: AAC76524.1
AP009048 Genomic DNA Translation: BAE77795.1
PIRiS47719
RefSeqiNP_417956.1, NC_000913.3
WP_001300574.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC76524; AAC76524; b3499
BAE77795; BAE77795; BAE77795
GeneIDi948012
KEGGiecj:JW3466
eco:b3499
PATRICifig|511145.12.peg.3601

Similar proteinsi

Entry informationi

Entry nameiRLMJ_ECOLI
AccessioniPrimary (citable) accession number: P37634
Secondary accession number(s): Q2M7G1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: March 28, 2018
This is version 129 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

3D-structure, Complete proteome, Reference proteome

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