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Protein

Ribosomal RNA large subunit methyltransferase J

Gene

rlmJ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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. Seems to be required for the utilization of extracellular DNA as the sole source of carbon and energy.UniRule annotation3 Publications

Catalytic activityi

S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + N(6)-methyladenine(2030) in 23S rRNA.UniRule annotation2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei19 – 191S-adenosyl-L-methionine1 Publication
Binding sitei42 – 421S-adenosyl-L-methionine; via carbonyl oxygen1 Publication
Binding sitei100 – 1001S-adenosyl-L-methionine1 Publication
Binding sitei118 – 1181S-adenosyl-L-methionine1 Publication
Active sitei164 – 1641Proton acceptor1 Publication
Binding sitei164 – 1641S-adenosyl-L-methionine1 Publication

GO - Molecular functioni

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

GO - Biological processi

  • carbon utilization Source: EcoCyc
  • rRNA base methylation Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG12234-MONOMER.
ECOL316407:JW3466-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12234. rlmJ.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

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 at 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). Cells lacking this gene are unable to grow using DNA as a sole nutrition source (PubMed:16707682).2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi4 – 41Y → A: Loss of catalytic activity. 1 Publication
Mutagenesisi4 – 41Y → F: 40-fold reduction in catalytic activity. 1 Publication
Mutagenesisi6 – 61H → D: Loss of catalytic activity. 1 Publication
Mutagenesisi18 – 181K → A: Loss of catalytic activity. 1 Publication
Mutagenesisi18 – 181K → R: 10-fold reduction in catalytic activity. 1 Publication
Mutagenesisi164 – 1641D → A: Loss of catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 280280Ribosomal RNA large subunit methyltransferase JPRO_0000169567Add
BLAST

Proteomic databases

PaxDbiP37634.

Interactioni

Subunit structurei

Monomer.UniRule annotation1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei4 – 41Interaction with substrate rRNACurated

Protein-protein interaction databases

BioGridi4262505. 7 interactions.
DIPiDIP-12371N.
IntActiP37634. 20 interactions.
MINTiMINT-1219143.
STRINGi511145.b3499.

Structurei

Secondary structure

1
280
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 83Combined sources
Turni9 – 113Combined sources
Helixi13 – 2917Combined sources
Beta strandi32 – 343Combined sources
Beta strandi37 – 426Combined sources
Beta strandi45 – 495Combined sources
Beta strandi53 – 564Combined sources
Helixi60 – 634Combined sources
Helixi65 – 673Combined sources
Turni68 – 703Combined sources
Helixi76 – 783Combined sources
Helixi79 – 879Combined sources
Turni88 – 914Combined sources
Beta strandi96 – 983Combined sources
Helixi100 – 1078Combined sources
Beta strandi113 – 1175Combined sources
Helixi123 – 1308Combined sources
Turni131 – 1333Combined sources
Beta strandi137 – 1404Combined sources
Turni144 – 1463Combined sources
Helixi147 – 1504Combined sources
Beta strandi159 – 1635Combined sources
Helixi170 – 18617Combined sources
Beta strandi190 – 20011Combined sources
Helixi201 – 21313Combined sources
Beta strandi219 – 2279Combined sources
Beta strandi231 – 2344Combined sources
Beta strandi237 – 2448Combined sources
Helixi249 – 26416Combined sources
Beta strandi270 – 2789Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BLUX-ray1.85A/B1-280[»]
4BLVX-ray2.00A/B1-280[»]
4BLWX-ray1.95A/B1-280[»]
ProteinModelPortaliP37634.
SMRiP37634. Positions 2-280.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni143 – 1442S-adenosyl-L-methionine binding1 Publication

Sequence similaritiesi

Belongs to the RlmJ family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105D6S. Bacteria.
COG2961. LUCA.
HOGENOMiHOG000262479.
InParanoidiP37634.
KOiK07115.
OMAiTYAIWYP.
PhylomeDBiP37634.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_00934. 23SrRNA_methyltr_J. 1 hit.
InterProiIPR002052. DNA_methylase_N6_adenine_CS.
IPR007473. RlmJ.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF04378. RsmJ. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS00092. N6_MTASE. 2 hits.
[Graphical view]

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.
PATRICi32122448. VBIEscCol129921_3601.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BLUX-ray1.85A/B1-280[»]
4BLVX-ray2.00A/B1-280[»]
4BLWX-ray1.95A/B1-280[»]
ProteinModelPortaliP37634.
SMRiP37634. Positions 2-280.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262505. 7 interactions.
DIPiDIP-12371N.
IntActiP37634. 20 interactions.
MINTiMINT-1219143.
STRINGi511145.b3499.

Proteomic databases

PaxDbiP37634.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76524; AAC76524; b3499.
BAE77795; BAE77795; BAE77795.
GeneIDi948012.
KEGGiecj:JW3466.
eco:b3499.
PATRICi32122448. VBIEscCol129921_3601.

Organism-specific databases

EchoBASEiEB2146.
EcoGeneiEG12234. rlmJ.

Phylogenomic databases

eggNOGiENOG4105D6S. Bacteria.
COG2961. LUCA.
HOGENOMiHOG000262479.
InParanoidiP37634.
KOiK07115.
OMAiTYAIWYP.
PhylomeDBiP37634.

Enzyme and pathway databases

BioCyciEcoCyc:EG12234-MONOMER.
ECOL316407:JW3466-MONOMER.
MetaCyc:EG12234-MONOMER.
BRENDAi2.1.1.266. 2026.

Miscellaneous databases

PROiP37634.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_00934. 23SrRNA_methyltr_J. 1 hit.
InterProiIPR002052. DNA_methylase_N6_adenine_CS.
IPR007473. RlmJ.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PfamiPF04378. RsmJ. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS00092. N6_MTASE. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRLMJ_ECOLI
AccessioniPrimary (citable) accession number: P37634
Secondary accession number(s): Q2M7G1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: September 7, 2016
This is version 118 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.