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Protein

Ribosomal RNA small subunit methyltransferase D

Gene

rsmD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates the guanine in position 966 of 16S rRNA in the assembled 30S particle.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + guanine(966) in 16S rRNA = S-adenosyl-L-homocysteine + N(2)-methylguanine(966) in 16S rRNA.

GO - Molecular functioni

GO - Biological processi

  • rRNA base methylation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG10343-MONOMER.
ECOL316407:JW3430-MONOMER.
MetaCyc:EG10343-MONOMER.
BRENDAi2.1.1.171. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA small subunit methyltransferase D (EC:2.1.1.171)
Alternative name(s):
16S rRNA m2G966 methyltransferase
rRNA (guanine-N(2)-)-methyltransferase
Gene namesi
Name:rsmD
Synonyms:yhhF
Ordered Locus Names:b3465, JW3430
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10343. rsmD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 198198Ribosomal RNA small subunit methyltransferase DPRO_0000169548Add
BLAST

Proteomic databases

PaxDbiP0ADX9.
PRIDEiP0ADX9.

2D gel databases

SWISS-2DPAGEP0ADX9.

Interactioni

Protein-protein interaction databases

BioGridi4262500. 46 interactions.
DIPiDIP-48275N.
IntActiP0ADX9. 6 interactions.
MINTiMINT-1267285.
STRINGi511145.b3465.

Structurei

Secondary structure

1
198
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 133Combined sources
Helixi17 – 193Combined sources
Beta strandi23 – 253Combined sources
Helixi37 – 5115Combined sources
Beta strandi55 – 584Combined sources
Helixi65 – 728Combined sources
Beta strandi76 – 816Combined sources
Helixi85 – 9713Combined sources
Beta strandi102 – 1065Combined sources
Helixi110 – 1145Combined sources
Beta strandi121 – 1266Combined sources
Beta strandi129 – 1313Combined sources
Turni132 – 1343Combined sources
Helixi135 – 14410Combined sources
Beta strandi148 – 15912Combined sources
Helixi160 – 1623Combined sources
Beta strandi171 – 1799Combined sources
Beta strandi182 – 1898Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FPOX-ray2.05A/B/C/D/E/F1-198[»]
ProteinModelPortaliP0ADX9.
SMRiP0ADX9. Positions 10-192.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0ADX9.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4106H78. Bacteria.
COG0742. LUCA.
HOGENOMiHOG000050676.
InParanoidiP0ADX9.
KOiK08316.
OMAiMVDARCL.
OrthoDBiEOG64XXSX.
PhylomeDBiP0ADX9.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR002052. DNA_methylase_N6_adenine_CS.
IPR004398. RNA_MeTrfase_RsmD.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PIRSFiPIRSF004553. CHP00095. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00095. TIGR00095. 1 hit.
PROSITEiPS00092. N6_MTASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0ADX9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKPNHSGSG QIRIIGGQWR GRKLPVPDSP GLRPTTDRVR ETLFNWLAPV
60 70 80 90 100
IVDAQCLDCF AGSGALGLEA LSRYAAGATL IEMDRAVSQQ LIKNLATLKA
110 120 130 140 150
GNARVVNSNA MSFLAQKGTP HNIVFVDPPF RRGLLEETIN LLEDNGWLAD
160 170 180 190
EALIYVESEV ENGLPTVPAN WSLHREKVAG QVAYRLYQRE AQGESDAD
Length:198
Mass (Da):21,678
Last modified:December 6, 2005 - v1
Checksum:i04FB9D9DAF972605
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04398 Genomic DNA. Translation: CAA27983.1.
U00039 Genomic DNA. Translation: AAB18440.1.
U00096 Genomic DNA. Translation: AAC76490.1.
AP009048 Genomic DNA. Translation: BAE77828.1.
PIRiS03129. QQECX3.
RefSeqiNP_417922.1. NC_000913.3.
WP_000743193.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76490; AAC76490; b3465.
BAE77828; BAE77828; BAE77828.
GeneIDi947977.
KEGGiecj:JW3430.
eco:b3465.
PATRICi32122374. VBIEscCol129921_3564.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04398 Genomic DNA. Translation: CAA27983.1.
U00039 Genomic DNA. Translation: AAB18440.1.
U00096 Genomic DNA. Translation: AAC76490.1.
AP009048 Genomic DNA. Translation: BAE77828.1.
PIRiS03129. QQECX3.
RefSeqiNP_417922.1. NC_000913.3.
WP_000743193.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FPOX-ray2.05A/B/C/D/E/F1-198[»]
ProteinModelPortaliP0ADX9.
SMRiP0ADX9. Positions 10-192.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262500. 46 interactions.
DIPiDIP-48275N.
IntActiP0ADX9. 6 interactions.
MINTiMINT-1267285.
STRINGi511145.b3465.

2D gel databases

SWISS-2DPAGEP0ADX9.

Proteomic databases

PaxDbiP0ADX9.
PRIDEiP0ADX9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76490; AAC76490; b3465.
BAE77828; BAE77828; BAE77828.
GeneIDi947977.
KEGGiecj:JW3430.
eco:b3465.
PATRICi32122374. VBIEscCol129921_3564.

Organism-specific databases

EchoBASEiEB0339.
EcoGeneiEG10343. rsmD.

Phylogenomic databases

eggNOGiENOG4106H78. Bacteria.
COG0742. LUCA.
HOGENOMiHOG000050676.
InParanoidiP0ADX9.
KOiK08316.
OMAiMVDARCL.
OrthoDBiEOG64XXSX.
PhylomeDBiP0ADX9.

Enzyme and pathway databases

BioCyciEcoCyc:EG10343-MONOMER.
ECOL316407:JW3430-MONOMER.
MetaCyc:EG10343-MONOMER.
BRENDAi2.1.1.171. 2026.

Miscellaneous databases

EvolutionaryTraceiP0ADX9.
PROiP0ADX9.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR002052. DNA_methylase_N6_adenine_CS.
IPR004398. RNA_MeTrfase_RsmD.
IPR029063. SAM-dependent_MTases.
[Graphical view]
PIRSFiPIRSF004553. CHP00095. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00095. TIGR00095. 1 hit.
PROSITEiPS00092. N6_MTASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A new cell division operon in Escherichia coli."
    Gill D.R., Hatfull G.F., Salmond G.P.C.
    Mol. Gen. Genet. 205:134-145(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes."
    Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.
    Nucleic Acids Res. 22:2576-2586(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. 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. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  6. "Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure."
    Lesnyak D.V., Osipiuk J., Skarina T., Sergiev P.V., Bogdanov A.A., Edwards A., Savchenko A., Joachimiak A., Dontsova O.A.
    J. Biol. Chem. 282:5880-5887(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS), FUNCTION.

Entry informationi

Entry nameiRSMD_ECOLI
AccessioniPrimary (citable) accession number: P0ADX9
Secondary accession number(s): P10120, Q2M7C8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: December 6, 2005
Last modified: July 6, 2016
This is version 89 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.