Ribosomal RNA small subunit methyltransferase B - Escherichia coli (strain K12)

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P36929 (RSMB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 126. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Ribosomal RNA small subunit methyltransferase B
EC=2.1.1.176

Alternative name(s):
16S rRNA m5C967 methyltransferase
rRNA (cytosine-C(5)-)-methyltransferase RsmB

Gene names

Name:	rsmB
Synonyms:	fmu/fmv, rrmB, sun, yhdB
Ordered Locus Names:	b3289, JW3250

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	429 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA. Ref.7
Catalytic activity	S-adenosyl-L-methionine + cytosine(967) in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(967) in 16S rRNA. HAMAP-Rule MF_01856
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01856.
Sequence similarities	Belongs to the methyltransferase superfamily. RsmB/NOP family.
Sequence caution	The sequence AAA58086.1 differs from that shown. Reason: Frameshift at position 384. The sequence CAA54369.1 differs from that shown. Reason: Frameshift at position 201. Was originally named Fmu and represented the N-terminal part of the RsmB protein. The sequence CAA54370.1 differs from that shown. Reason: Frameshift at position 201. Was originally named Fmv and represented the C-terminal part of the RsmB protein.

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 Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	rRNA base methylation Inferred from mutant phenotype Ref.7. Source: EcoCyc regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW rRNA (cytosine-C5-)-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 – 429

429

Ribosomal RNA small subunit methyltransferase B HAMAP-Rule MF_01856

PRO_0000211792

Regions

Region

254 – 260

S-adenosyl-L-methionine binding HAMAP-Rule MF_01856

Sites

Active site

375

Nucleophile Potential

Binding site

277

S-adenosyl-L-methionine

Binding site

303

S-adenosyl-L-methionine

Binding site

322

S-adenosyl-L-methionine

Experimental info

Mutagenesis

325

C → A: Reduces activity 3-fold. Ref.8 Ref.9

Mutagenesis

375

C → A: Loss of activity. Ref.8 Ref.9

Sequence conflict

K → C AA sequence Ref.6

Sequence conflict

K → W AA sequence Ref.6

Sequence conflict

105 – 106

GA → RR in CAA54369. Ref.1

Secondary structure

429

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P36929 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: 1F516223C84D80F8
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FASTA

429

48,348

        10         20         30         40         50         60 
MKKQRNLRSM AAQAVEQVVE QGQSLSNILP PLQQKVSDKD KALLQELCFG VLRTLSQLDW 

        70         80         90        100        110        120 
LINKLMARPM TGKQRTVHYL IMVGLYQLLY TRIPPHAALA ETVEGAIAIK RPQLKGLING 

       130        140        150        160        170        180 
VLRQFQRQQE ELLAEFNASD ARYLHPSWLL KRLQKAYPEQ WQSIVEANNQ RPPMWLRINR 

       190        200        210        220        230        240 
THHSRDSWLA LLDEAGMKGF PHADYPDAVR LETPAPVHAL PGFEDGWVTV QDASAQGCMT 

       250        260        270        280        290        300 
WLAPQNGEHI LDLCAAPGGK TTHILEVAPE AQVVAVDIDE QRLSRVYDNL KRLGMKATVK 

       310        320        330        340        350        360 
QGDGRYPSQW CGEQQFDRIL LDAPCSATGV IRRHPDIKWL RRDRDIPELA QLQSEILDAI 

       370        380        390        400        410        420 
WPHLKTGGTL VYATCSVLPE ENSLQIKAFL QRTADAELCE TGTPEQPGKQ NLPGAEEGDG 


FFYAKLIKK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet) formyltransferase, escapes metabolic control." Meinnel T., Guillon J.-M., Mechulam Y., Blanquet S. J. Bacteriol. 175:993-1000(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / K37.
[2]	"A survey of polypeptide deformylase function throughout the eubacterial lineage." Mazel D., Coic E., Blanchard S., Saurin W., Marliere P. J. Mol. Biol. 266:939-949(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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.
[4]	"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.
[5]	"NAD+ binding to the Escherichia coli K(+)-uptake protein TrkA and sequence similarity between TrkA and domains of a family of dehydrogenases suggest a role for NAD+ in bacterial transport." Schloesser A., Hamann A., Bossemeyer D., Schneider E., Bakker E.P. Mol. Microbiol. 9:533-543(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 384-429.
[6]	"Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli." Tscherne J.S., Nurse K., Popienick P., Michel H., Sochacki M., Ofengand J. Biochemistry 38:1884-1892(1999) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-23 AND 418-429, CHARACTERIZATION.
[7]	"Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli." Gu X.R., Gustafsson C., Ku J., Yu M., Santi D.V. Biochemistry 38:4053-4057(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[8]	"m5C RNA and m5C DNA methyl transferases use different cysteine residues as catalysts." Liu Y., Santi D.V. Proc. Natl. Acad. Sci. U.S.A. 97:8263-8265(2000) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYS-325 AND CYS-375, ACTIVE SITE.
[9]	"The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate." Foster P.G., Nunes C.R., Greene P., Moustakas D., Stroud R.M. Structure 11:1609-1620(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE, MUTAGENESIS OF CYS-325 AND CYS-375.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X77091 Genomic DNA. Translation: CAA54369.1. Frameshift.
X77091 Genomic DNA. Translation: CAA54370.1. Frameshift.
Y10307 Genomic DNA. Translation: CAA71359.1.
U18997 Genomic DNA. Translation: AAA58086.1. Frameshift.
U00096 Genomic DNA. Translation: AAC76314.1.
AP009048 Genomic DNA. Translation: BAE78003.1.
X52114 Genomic DNA. Translation: CAA36358.1.

PIR

D65121.

RefSeq

NP_417747.1. NC_000913.2.
YP_492144.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1J4F	model	-	A	228-429	[»]
1SQF	X-ray	2.10	A	1-429	[»]
1SQG	X-ray	1.65	A	1-429	[»]

ProteinModelPortal

P36929.

SMR

P36929. Positions 5-428.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10946N.

IntAct

P36929. 14 interactions.

STRING

511145.b3289.

Proteomic databases

PaxDb

P36929.

PRIDE

P36929.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76314; AAC76314; b3289.
BAE78003; BAE78003; BAE78003.

GeneID

12934442.
947789.

KEGG

ecj:Y75_p3888.
eco:b3289.

PATRIC

32122010. VBIEscCol129921_3382.

Organism-specific databases

EchoBASE

EB2082.

EcoGene

EG12163. rsmB.

Phylogenomic databases

eggNOG

COG0144.

HOGENOM

HOG000037300.

K03500.

OMA

KPPMWLR.

ProtClustDB

PRK10901.

Enzyme and pathway databases

BioCyc

EcoCyc:EG12163-MONOMER.
ECOL316407:JW3250-MONOMER.
MetaCyc:EG12163-MONOMER.

Gene expression databases

Genevestigator

P36929.

Family and domain databases

Gene3D

1.10.940.10. 1 hit.

HAMAP

MF_01856. 16SrRNA_methyltr_B.

InterPro

IPR001678. Fmu/NOL1/Nop2p.
IPR018314. Fmu/NOL1/Nop2p_CS.
IPR006027. NusB_RsmB_TIM44.
IPR023267. RCMT.
IPR004573. rRNA_ssu_MeTfrase_B.
IPR023541. rRNA_ssu_MeTfrase_B_ent.
[Graphical view]

Pfam

PF01189. Nol1_Nop2_Fmu. 1 hit.
PF01029. NusB. 1 hit.
[Graphical view]

PRINTS

PR02008. RCMTFAMILY.

SUPFAM

SSF48013. NusB_RsmB_TIM44. 1 hit.

TIGRFAMs

TIGR00563. rsmB. 1 hit.

PROSITE

PS01153. NOL1_NOP2_SUN. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P36929.

Entry information

Entry name

RSMB_ECOLI

Accession

Primary (citable) accession number: P36929
Secondary accession number(s): P23866, Q2M6V3

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	November 1, 1995
Last modified:	May 1, 2013
This is version 126 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents