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Protein

Ribosomal RNA large subunit methyltransferase K/L

Gene

rlmL

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA. Methylation occurs before assembly of 23S rRNA into 50S subunits.3 Publications

Catalytic activityi

S-adenosyl-L-methionine + guanine(2445) in 23S rRNA = S-adenosyl-L-homocysteine + N(2)-methylguanine(2445) in 23S rRNA.
S-adenosyl-L-methionine + guanine(2069) in 23S rRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(2069) in 23S rRNA.

Enzyme regulationi

The N-terminal RlmL activity is enhanced by the C-terminal RlmK activity.1 Publication

GO - Molecular functioni

GO - Biological processi

  • rRNA base methylation Source: EcoCyc
  • rRNA 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:G6488-MONOMER.
ECOL316407:JW0931-MONOMER.
MetaCyc:G6488-MONOMER.
BRENDAi2.1.1.173. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA large subunit methyltransferase K/L
Including the following 2 domains:
23S rRNA m2G2445 methyltransferase (EC:2.1.1.173)
Alternative name(s):
rRNA (guanine-N(2)-)-methyltransferase RlmL
23S rRNA m7G2069 methyltransferase (EC:2.1.1.264)
Alternative name(s):
rRNA (guanine-N(7)-)-methyltransferase RlmK
Gene namesi
Name:rlmL
Synonyms:rlmK, rlmKL, ycbY
Ordered Locus Names:b0948, JW0931
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13717. rlmL.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi195D → A: Does not affect methyltransferase activity. 1 Publication1
Mutagenesisi309N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. 1 Publication1
Mutagenesisi397N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. 1 Publication1
Mutagenesisi530R → A: Does not affect methyltransferase activity. 1 Publication1
Mutagenesisi568D → A: Impairs m7G2069 formation, but does not affect m2G2445 formation. 1 Publication1
Mutagenesisi597D → A: Does not affect methyltransferase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001404731 – 702Ribosomal RNA large subunit methyltransferase K/LAdd BLAST702

Proteomic databases

PaxDbiP75864.
PRIDEiP75864.

Interactioni

Subunit structurei

Monomer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
typAP321323EBI-547718,EBI-562154

Protein-protein interaction databases

BioGridi4260025. 122 interactors.
DIPiDIP-11486N.
IntActiP75864. 48 interactors.
MINTiMINT-1268879.
STRINGi511145.b0948.

Structurei

Secondary structure

1702
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Helixi13 – 22Combined sources10
Beta strandi26 – 31Combined sources6
Beta strandi34 – 39Combined sources6
Helixi41 – 50Combined sources10
Beta strandi55 – 65Combined sources11
Helixi69 – 77Combined sources9
Helixi81 – 84Combined sources4
Beta strandi91 – 96Combined sources6
Helixi105 – 121Combined sources17
Turni122 – 124Combined sources3
Beta strandi132 – 134Combined sources3
Beta strandi136 – 144Combined sources9
Beta strandi147 – 157Combined sources11
Beta strandi163 – 165Combined sources3
Helixi175 – 184Combined sources10
Beta strandi193 – 195Combined sources3
Helixi202 – 211Combined sources10
Turni216 – 219Combined sources4
Turni224 – 227Combined sources4
Helixi233 – 253Combined sources21
Beta strandi258 – 263Combined sources6
Helixi265 – 277Combined sources13
Helixi281 – 283Combined sources3
Beta strandi284 – 288Combined sources5
Helixi291 – 293Combined sources3
Beta strandi305 – 308Combined sources4
Helixi320 – 336Combined sources17
Beta strandi341 – 347Combined sources7
Helixi349 – 353Combined sources5
Beta strandi359 – 367Combined sources9
Beta strandi370 – 378Combined sources9
Helixi393 – 413Combined sources21
Beta strandi417 – 423Combined sources7
Beta strandi430 – 435Combined sources6
Beta strandi438 – 443Combined sources6
Helixi454 – 470Combined sources17
Helixi474 – 476Combined sources3
Beta strandi477 – 480Combined sources4
Beta strandi501 – 505Combined sources5
Beta strandi508 – 512Combined sources5
Beta strandi514 – 519Combined sources6
Helixi524 – 526Combined sources3
Helixi527 – 536Combined sources10
Beta strandi541 – 546Combined sources6
Helixi551 – 558Combined sources8
Beta strandi562 – 569Combined sources8
Helixi571 – 583Combined sources13
Beta strandi591 – 596Combined sources6
Helixi598 – 604Combined sources7
Beta strandi609 – 614Combined sources6
Helixi631 – 645Combined sources15
Beta strandi646 – 656Combined sources11
Helixi665 – 670Combined sources6
Beta strandi673 – 677Combined sources5
Turni679 – 682Combined sources4
Helixi685 – 687Combined sources3
Beta strandi695 – 701Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3V8VX-ray2.60A/B1-702[»]
3V97X-ray2.20A/B1-702[»]
ProteinModelPortaliP75864.
SMRiP75864.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini43 – 154THUMPAdd BLAST112

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 397RlmLAdd BLAST397
Regioni398 – 702RlmKAdd BLAST305

Domaini

Consists of a N-terminal RlmL domain and a C-terminal RlmK domain, linked by a highly flexible loop.2 Publications

Sequence similaritiesi

Contains 1 THUMP domain.Curated

Phylogenomic databases

eggNOGiENOG4105C4H. Bacteria.
COG0116. LUCA.
COG1092. LUCA.
HOGENOMiHOG000218371.
InParanoidiP75864.
KOiK12297.
OMAiMSNTYLN.
PhylomeDBiP75864.

Family and domain databases

Gene3Di3.40.50.150. 3 hits.
HAMAPiMF_01858. 23SrRNA_methyltr_KL. 1 hit.
InterProiIPR017244. 23SrRNA_methyltr_KL.
IPR002052. DNA_methylase_N6_adenine_CS.
IPR000241. RNA_methylase_dom.
IPR019614. SAM-dep_methyl-trfase.
IPR029063. SAM-dependent_MTases.
IPR004114. THUMP_dom.
[Graphical view]
PfamiPF10672. Methyltrans_SAM. 1 hit.
PF02926. THUMP. 1 hit.
PF01170. UPF0020. 1 hit.
[Graphical view]
PIRSFiPIRSF037618. RNA_Mtase_bacteria_prd. 1 hit.
SMARTiSM00981. THUMP. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 3 hits.
PROSITEiPS51165. THUMP. 1 hit.
PS01261. UPF0020. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P75864-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSLFASTAR GLEELLKTEL ENLGAVECQV VQGGVHFKGD TRLVYQSLMW
60 70 80 90 100
SRLASRIMLP LGECKVYSDL DLYLGVQAIN WTEMFNPGAT FAVHFSGLND
110 120 130 140 150
TIRNSQYGAM KVKDAIVDAF TRKNLPRPNV DRDAPDIRVN VWLHKETASI
160 170 180 190 200
ALDLSGDGLH LRGYRDRAGI APIKETLAAA IVMRSGWQPG TPLLDPMCGS
210 220 230 240 250
GTLLIEAAML ATDRAPGLHR GRWGFSGWAQ HDEAIWQEVK AEAQTRARKG
260 270 280 290 300
LAEYSSHFYG SDSDARVIQR ARTNARLAGI GELITFEVKD VAQLTNPLPK
310 320 330 340 350
GPYGTVLSNP PYGERLDSEP ALIALHSLLG RIMKNQFGGW NLSLFSASPD
360 370 380 390 400
LLSCLQLRAD KQYKAKNGPL DCVQKNYHVA ESTPDSKPAM VAEDYTNRLR
410 420 430 440 450
KNLKKFEKWA RQEGIECYRL YDADLPEYNV AVDRYADWVV VQEYAPPKTI
460 470 480 490 500
DAHKARQRLF DIIAATISVL GIAPNKLVLK TRERQKGKNQ YQKLGEKGEF
510 520 530 540 550
LEVTEYNAHL WVNLTDYLDT GLFLDHRIAR RMLGQMSKGK DFLNLFSYTG
560 570 580 590 600
SATVHAGLGG ARSTTTVDMS RTYLEWAERN LRLNGLTGRA HRLIQADCLA
610 620 630 640 650
WLREANEQFD LIFIDPPTFS NSKRMEDAFD VQRDHLALMK DLKRLLRAGG
660 670 680 690 700
TIMFSNNKRG FRMDLDGLAK LGLKAQEITQ KTLSQDFARN RQIHNCWLIT

AA
Length:702
Mass (Da):78,854
Last modified:February 1, 1997 - v1
Checksum:i9EF24AD7A32AC429
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74034.1.
AP009048 Genomic DNA. Translation: BAA35703.1.
PIRiC64835.
RefSeqiNP_415468.1. NC_000913.3.
WP_001086539.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74034; AAC74034; b0948.
BAA35703; BAA35703; BAA35703.
GeneIDi945564.
KEGGiecj:JW0931.
eco:b0948.
PATRICi32117115. VBIEscCol129921_0982.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74034.1.
AP009048 Genomic DNA. Translation: BAA35703.1.
PIRiC64835.
RefSeqiNP_415468.1. NC_000913.3.
WP_001086539.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3V8VX-ray2.60A/B1-702[»]
3V97X-ray2.20A/B1-702[»]
ProteinModelPortaliP75864.
SMRiP75864.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260025. 122 interactors.
DIPiDIP-11486N.
IntActiP75864. 48 interactors.
MINTiMINT-1268879.
STRINGi511145.b0948.

Proteomic databases

PaxDbiP75864.
PRIDEiP75864.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74034; AAC74034; b0948.
BAA35703; BAA35703; BAA35703.
GeneIDi945564.
KEGGiecj:JW0931.
eco:b0948.
PATRICi32117115. VBIEscCol129921_0982.

Organism-specific databases

EchoBASEiEB3481.
EcoGeneiEG13717. rlmL.

Phylogenomic databases

eggNOGiENOG4105C4H. Bacteria.
COG0116. LUCA.
COG1092. LUCA.
HOGENOMiHOG000218371.
InParanoidiP75864.
KOiK12297.
OMAiMSNTYLN.
PhylomeDBiP75864.

Enzyme and pathway databases

BioCyciEcoCyc:G6488-MONOMER.
ECOL316407:JW0931-MONOMER.
MetaCyc:G6488-MONOMER.
BRENDAi2.1.1.173. 2026.

Miscellaneous databases

PROiP75864.

Family and domain databases

Gene3Di3.40.50.150. 3 hits.
HAMAPiMF_01858. 23SrRNA_methyltr_KL. 1 hit.
InterProiIPR017244. 23SrRNA_methyltr_KL.
IPR002052. DNA_methylase_N6_adenine_CS.
IPR000241. RNA_methylase_dom.
IPR019614. SAM-dep_methyl-trfase.
IPR029063. SAM-dependent_MTases.
IPR004114. THUMP_dom.
[Graphical view]
PfamiPF10672. Methyltrans_SAM. 1 hit.
PF02926. THUMP. 1 hit.
PF01170. UPF0020. 1 hit.
[Graphical view]
PIRSFiPIRSF037618. RNA_Mtase_bacteria_prd. 1 hit.
SMARTiSM00981. THUMP. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 3 hits.
PROSITEiPS51165. THUMP. 1 hit.
PS01261. UPF0020. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRLMKL_ECOLI
AccessioniPrimary (citable) accession number: P75864
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: November 2, 2016
This is version 135 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.