P75864 (RLMKL_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribosomal RNA large subunit methyltransferase K/L

Including the following 2 domains:

1. 23S rRNA m2G2445 methyltransferase
   EC=2.1.1.173
   Alternative name(s):
   rRNA (guanine-N(2)-)-methyltransferase RlmL
2. 23S rRNA m7G2069 methyltransferase
   EC=2.1.1.264
   Alternative name(s):
   rRNA (guanine-N(7)-)-methyltransferase RlmK

Gene names

Name:	rlmL
Synonyms:	rlmK, rlmKL, ycbY
Ordered Locus Names:	b0948, JW0931

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	702 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.4 Ref.6 Ref.7
Catalytic activity	S-adenosyl-L-methionine + guanine(2445) in 23S rRNA = S-adenosyl-L-homocysteine + N(2)-methylguanine(2445) in 23S rRNA. Ref.4 Ref.6 Ref.7 S-adenosyl-L-methionine + guanine(2069) in 23S rRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(2069) in 23S rRNA. Ref.4 Ref.6 Ref.7
Enzyme regulation	The N-terminal RlmL activity is enhanced by the C-terminal RlmK activity. Ref.6
Subunit structure	Monomer. Ref.7
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01858.
Domain	Consists of a N-terminal RlmL domain and a C-terminal RlmK domain, linked by a highly flexible loop. Ref.6 Ref.7
Sequence similarities	Belongs to the methyltransferase superfamily. RlmKL family. Contains 1 THUMP domain.

Ontologies

Keywords
Biological process	rRNA processing
Cellular component	Cytoplasm
Ligand	RNA-binding S-adenosyl-L-methionine
Molecular function	Methyltransferase Transferase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Cellular_component	cytoplasm Inferred by curator Ref.4. Source: UniProtKB
Molecular_function	23S rRNA (guanine(2445)-N(2))-methyltransferase activity Inferred from electronic annotation. Source: HAMAP RNA binding Inferred from electronic annotation. Source: HAMAP rRNA (guanine-N2-)-methyltransferase activity Inferred from direct assay Ref.4. Source: UniProtKB rRNA (guanine-N7-)-methyltransferase activity Inferred from direct assay Ref.6. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 702

702

Ribosomal RNA large subunit methyltransferase K/L HAMAP-Rule MF_01858

PRO_0000140473

Regions

Domain

43 – 154

112

THUMP

Region

1 – 397

397

RlmL HAMAP-Rule MF_01858

Region

398 – 702

305

RlmK HAMAP-Rule MF_01858

Experimental info

Mutagenesis

195

1

D → A: Does not affect methyltransferase activity. Ref.6

Mutagenesis

309

1

N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. Ref.6

Mutagenesis

397

1

N → A: Impairs m2G2445 formation, but does not affect m7G2069 formation. Ref.6

Mutagenesis

530

1

R → A: Does not affect methyltransferase activity. Ref.6

Mutagenesis

568

1

D → A: Impairs m7G2069 formation, but does not affect m2G2445 formation. Ref.6

Mutagenesis

597

1

D → A: Does not affect methyltransferase activity. Ref.6

Secondary structure

1

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702

Helix Strand Turn

Details...

Beta strand

2 – 7

6

Helix

13 – 22

10

Beta strand

26 – 31

6

Beta strand

34 – 39

6

Helix

41 – 50

10

Beta strand

55 – 65

11

Helix

69 – 77

9

Helix

81 – 84

4

Beta strand

91 – 96

6

Helix

105 – 121

17

Turn

122 – 124

3

Beta strand

132 – 134

3

Beta strand

136 – 144

9

Beta strand

147 – 157

11

Beta strand

163 – 165

3

Helix

175 – 184

10

Beta strand

193 – 195

3

Helix

202 – 211

10

Turn

216 – 219

4

Turn

224 – 227

4

Helix

233 – 253

21

Beta strand

258 – 263

6

Helix

265 – 277

13

Helix

281 – 283

3

Beta strand

284 – 288

5

Helix

291 – 293

3

Beta strand

305 – 308

4

Helix

320 – 336

17

Beta strand

341 – 347

7

Helix

349 – 353

5

Beta strand

359 – 367

9

Beta strand

370 – 378

9

Helix

393 – 413

21

Beta strand

417 – 423

7

Beta strand

430 – 435

6

Beta strand

438 – 443

6

Helix

454 – 470

17

Helix

474 – 476

3

Beta strand

477 – 480

4

Beta strand

501 – 505

5

Beta strand

508 – 512

5

Beta strand

514 – 519

6

Helix

524 – 526

3

Helix

527 – 536

10

Beta strand

541 – 546

6

Helix

551 – 558

8

Beta strand

562 – 569

8

Helix

571 – 583

13

Beta strand

591 – 596

6

Helix

598 – 604

7

Beta strand

609 – 614

6

Helix

631 – 645

15

Beta strand

646 – 656

11

Helix

665 – 670

6

Beta strand

673 – 677

5

Turn

679 – 682

4

Helix

685 – 687

3

Beta strand

695 – 701

7

Sequences

	Sequence		Length	Mass (Da)
	P75864 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: 9EF24AD7A32AC429	FASTA	702	78,854
	10 20 30 40 50 60 MNSLFASTAR GLEELLKTEL ENLGAVECQV VQGGVHFKGD TRLVYQSLMW SRLASRIMLP 70 80 90 100 110 120 LGECKVYSDL DLYLGVQAIN WTEMFNPGAT FAVHFSGLND TIRNSQYGAM KVKDAIVDAF 130 140 150 160 170 180 TRKNLPRPNV DRDAPDIRVN VWLHKETASI ALDLSGDGLH LRGYRDRAGI APIKETLAAA 190 200 210 220 230 240 IVMRSGWQPG TPLLDPMCGS GTLLIEAAML ATDRAPGLHR GRWGFSGWAQ HDEAIWQEVK 250 260 270 280 290 300 AEAQTRARKG LAEYSSHFYG SDSDARVIQR ARTNARLAGI GELITFEVKD VAQLTNPLPK 310 320 330 340 350 360 GPYGTVLSNP PYGERLDSEP ALIALHSLLG RIMKNQFGGW NLSLFSASPD LLSCLQLRAD 370 380 390 400 410 420 KQYKAKNGPL DCVQKNYHVA ESTPDSKPAM VAEDYTNRLR KNLKKFEKWA RQEGIECYRL 430 440 450 460 470 480 YDADLPEYNV AVDRYADWVV VQEYAPPKTI DAHKARQRLF DIIAATISVL GIAPNKLVLK 490 500 510 520 530 540 TRERQKGKNQ YQKLGEKGEF LEVTEYNAHL WVNLTDYLDT GLFLDHRIAR RMLGQMSKGK 550 560 570 580 590 600 DFLNLFSYTG SATVHAGLGG ARSTTTVDMS RTYLEWAERN LRLNGLTGRA HRLIQADCLA 610 620 630 640 650 660 WLREANEQFD LIFIDPPTFS NSKRMEDAFD VQRDHLALMK DLKRLLRAGG TIMFSNNKRG 670 680 690 700 FRMDLDGLAK LGLKAQEITQ KTLSQDFARN RQIHNCWLIT AA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U00096 Genomic DNA. Translation: AAC74034.1.
AP009048 Genomic DNA. Translation: BAA35703.1.

PIR

C64835.

RefSeq

NP_415468.1. NC_000913.2.
YP_489220.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P75864.

SMR

P75864. Positions 1-702.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11486N.

IntAct

P75864. 45 interactions.

MINT

MINT-1268879.

STRING

511145.b0948.

Proteomic databases

PaxDb

P75864.

PRIDE

P75864.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74034; AAC74034; b0948.
BAA35703; BAA35703; BAA35703.

GeneID

12931031.
945564.

KEGG

ecj:Y75_p0920.
eco:b0948.

PATRIC

32117115. VBIEscCol129921_0982.

Organism-specific databases

EchoBASE

EB3481.

EcoGene

EG13717. rlmL.

Phylogenomic databases

eggNOG

COG0116.

HOGENOM

HOG000218371.

KO

K12297.

OMA

NKRGFKM.

ProtClustDB

PRK11783.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P75864.

Family and domain databases

HAMAP

MF_01858. 23SrRNA_methyltr_KL.

InterPro

IPR002052. DNA_methylase_N6_adenine_CS.
IPR002296. N12N6_MeTrfase.
IPR000241. RNA_methylase_dom.
IPR017244. S-Ado-dep_RNA_MeTrfase_bac.
IPR019614. SAM-dep_methyl-trfase.
IPR004114. THUMP.
[Graphical view]

Pfam

PF10672. Methyltrans_SAM. 1 hit.
PF02926. THUMP. 1 hit.
PF01170. UPF0020. 1 hit.
[Graphical view]

PIRSF

PIRSF037618. RNA_Mtase_bacteria_prd. 1 hit.

PRINTS

PR00507. N12N6MTFRASE.

SMART

SM00981. THUMP. 1 hit.
[Graphical view]

PROSITE

PS51165. THUMP. 1 hit.
PS01261. UPF0020. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RLMKL_ECOLI

Accession

Primary (citable) accession number: P75864

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	February 1, 1997
Last modified:	May 1, 2013
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program