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P75864

- RLMKL_ECOLI

UniProt

P75864 - RLMKL_ECOLI

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Protein

Ribosomal RNA large subunit methyltransferase K/L

Gene

rlmL

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

  1. 23S rRNA (guanine(2445)-N(2))-methyltransferase activity Source: UniProtKB-HAMAP
  2. RNA binding Source: UniProtKB-HAMAP
  3. rRNA (guanine-N2-)-methyltransferase activity Source: UniProtKB
  4. rRNA (guanine-N7-)-methyltransferase activity Source: EcoCyc

GO - Biological processi

  1. rRNA (guanine-N7)-methylation Source: GOC
  2. rRNA base methylation Source: EcoCyc
  3. 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.

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG13717. rlmL.

Subcellular locationi

Cytoplasm Curated

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi195 – 1951D → A: Does not affect methyltransferase activity. 1 Publication
Mutagenesisi309 – 3091N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. 1 Publication
Mutagenesisi397 – 3971N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. 1 Publication
Mutagenesisi530 – 5301R → A: Does not affect methyltransferase activity. 1 Publication
Mutagenesisi568 – 5681D → A: Impairs m7G2069 formation, but does not affect m2G2445 formation. 1 Publication
Mutagenesisi597 – 5971D → A: Does not affect methyltransferase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 702702Ribosomal RNA large subunit methyltransferase K/LPRO_0000140473Add
BLAST

Proteomic databases

PaxDbiP75864.
PRIDEiP75864.

Expressioni

Gene expression databases

GenevestigatoriP75864.

Interactioni

Subunit structurei

Monomer.1 Publication

Binary interactionsi

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

Protein-protein interaction databases

DIPiDIP-11486N.
IntActiP75864. 48 interactions.
MINTiMINT-1268879.
STRINGi511145.b0948.

Structurei

Secondary structure

1
702
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76
Helixi13 – 2210
Beta strandi26 – 316
Beta strandi34 – 396
Helixi41 – 5010
Beta strandi55 – 6511
Helixi69 – 779
Helixi81 – 844
Beta strandi91 – 966
Helixi105 – 12117
Turni122 – 1243
Beta strandi132 – 1343
Beta strandi136 – 1449
Beta strandi147 – 15711
Beta strandi163 – 1653
Helixi175 – 18410
Beta strandi193 – 1953
Helixi202 – 21110
Turni216 – 2194
Turni224 – 2274
Helixi233 – 25321
Beta strandi258 – 2636
Helixi265 – 27713
Helixi281 – 2833
Beta strandi284 – 2885
Helixi291 – 2933
Beta strandi305 – 3084
Helixi320 – 33617
Beta strandi341 – 3477
Helixi349 – 3535
Beta strandi359 – 3679
Beta strandi370 – 3789
Helixi393 – 41321
Beta strandi417 – 4237
Beta strandi430 – 4356
Beta strandi438 – 4436
Helixi454 – 47017
Helixi474 – 4763
Beta strandi477 – 4804
Beta strandi501 – 5055
Beta strandi508 – 5125
Beta strandi514 – 5196
Helixi524 – 5263
Helixi527 – 53610
Beta strandi541 – 5466
Helixi551 – 5588
Beta strandi562 – 5698
Helixi571 – 58313
Beta strandi591 – 5966
Helixi598 – 6047
Beta strandi609 – 6146
Helixi631 – 64515
Beta strandi646 – 65611
Helixi665 – 6706
Beta strandi673 – 6775
Turni679 – 6824
Helixi685 – 6873
Beta strandi695 – 7017

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3V8VX-ray2.60A/B1-702[»]
3V97X-ray2.20A/B1-702[»]
ProteinModelPortaliP75864.
SMRiP75864. Positions 1-702.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini43 – 154112THUMPAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 397397RlmLAdd
BLAST
Regioni398 – 702305RlmKAdd
BLAST

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

eggNOGiCOG0116.
HOGENOMiHOG000218371.
InParanoidiP75864.
KOiK12297.
OMAiNKRGFKM.
OrthoDBiEOG6HJ238.
PhylomeDBiP75864.

Family and domain databases

Gene3Di3.40.50.150. 3 hits.
HAMAPiMF_01858. 23SrRNA_methyltr_KL.
InterProiIPR017244. 23SrRNA_methyltr_KL.
IPR002052. DNA_methylase_N6_adenine_CS.
IPR002296. N12N6_MeTrfase.
IPR000241. RNA_methylase_dom.
IPR019614. SAM-dep_methyl-trfase.
IPR029063. SAM-dependent_MTases-like.
IPR004114. THUMP.
[Graphical view]
PfamiPF10672. Methyltrans_SAM. 1 hit.
PF02926. THUMP. 1 hit.
PF01170. UPF0020. 1 hit.
[Graphical view]
PIRSFiPIRSF037618. RNA_Mtase_bacteria_prd. 1 hit.
PRINTSiPR00507. N12N6MTFRASE.
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:
EMBL
GenBank
DDBJ
Links Updated
U00096 Genomic DNA. Translation: AAC74034.1.
AP009048 Genomic DNA. Translation: BAA35703.1.
PIRiC64835.
RefSeqiNP_415468.1. NC_000913.3.
YP_489220.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74034; AAC74034; b0948.
BAA35703; BAA35703; BAA35703.
GeneIDi12931031.
945564.
KEGGiecj:Y75_p0920.
eco:b0948.
PATRICi32117115. VBIEscCol129921_0982.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U00096 Genomic DNA. Translation: AAC74034.1 .
AP009048 Genomic DNA. Translation: BAA35703.1 .
PIRi C64835.
RefSeqi NP_415468.1. NC_000913.3.
YP_489220.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3V8V X-ray 2.60 A/B 1-702 [» ]
3V97 X-ray 2.20 A/B 1-702 [» ]
ProteinModelPortali P75864.
SMRi P75864. Positions 1-702.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-11486N.
IntActi P75864. 48 interactions.
MINTi MINT-1268879.
STRINGi 511145.b0948.

Proteomic databases

PaxDbi P75864.
PRIDEi P75864.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74034 ; AAC74034 ; b0948 .
BAA35703 ; BAA35703 ; BAA35703 .
GeneIDi 12931031.
945564.
KEGGi ecj:Y75_p0920.
eco:b0948.
PATRICi 32117115. VBIEscCol129921_0982.

Organism-specific databases

EchoBASEi EB3481.
EcoGenei EG13717. rlmL.

Phylogenomic databases

eggNOGi COG0116.
HOGENOMi HOG000218371.
InParanoidi P75864.
KOi K12297.
OMAi NKRGFKM.
OrthoDBi EOG6HJ238.
PhylomeDBi P75864.

Enzyme and pathway databases

BioCyci EcoCyc:G6488-MONOMER.
ECOL316407:JW0931-MONOMER.
MetaCyc:G6488-MONOMER.

Miscellaneous databases

PROi P75864.

Gene expression databases

Genevestigatori P75864.

Family and domain databases

Gene3Di 3.40.50.150. 3 hits.
HAMAPi MF_01858. 23SrRNA_methyltr_KL.
InterProi IPR017244. 23SrRNA_methyltr_KL.
IPR002052. DNA_methylase_N6_adenine_CS.
IPR002296. N12N6_MeTrfase.
IPR000241. RNA_methylase_dom.
IPR019614. SAM-dep_methyl-trfase.
IPR029063. SAM-dependent_MTases-like.
IPR004114. THUMP.
[Graphical view ]
Pfami PF10672. Methyltrans_SAM. 1 hit.
PF02926. THUMP. 1 hit.
PF01170. UPF0020. 1 hit.
[Graphical view ]
PIRSFi PIRSF037618. RNA_Mtase_bacteria_prd. 1 hit.
PRINTSi PR00507. N12N6MTFRASE.
SMARTi SM00981. THUMP. 1 hit.
[Graphical view ]
SUPFAMi SSF53335. SSF53335. 3 hits.
PROSITEi PS51165. THUMP. 1 hit.
PS01261. UPF0020. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA."
    Lesnyak D.V., Sergiev P.V., Bogdanov A.A., Dontsova O.A.
    J. Mol. Biol. 364:20-25(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  5. "Purification, crystallization and preliminary X-ray crystallographic analysis of 23S RNA m(2)G2445 methyltransferase RlmL from Escherichia coli."
    Wang K.T., Ma L., Nan J., Su X.D., Li L.
    Acta Crystallogr. F 66:1484-1486(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION.
  6. "Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity."
    Kimura S., Ikeuchi Y., Kitahara K., Sakaguchi Y., Suzuki T., Suzuki T.
    Nucleic Acids Res. 40:4071-4085(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, DOMAIN, MUTAGENESIS OF ASP-195; ASN-309; ASN-397; ARG-530; ASP-568 AND ASP-597.
  7. "Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA."
    Wang K.T., Desmolaize B., Nan J., Zhang X.W., Li L.F., Douthwaite S., Su X.D.
    Nucleic Acids Res. 40:5138-5148(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, DOMAIN.

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: October 29, 2014
This is version 120 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

External Data

Dasty 3