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Escherichia coli K-12 substr. MG1655 Enzyme: 16S rRNA m2G966 methyltransferase



Gene: rsmD Accession Numbers: EG10343 (EcoCyc), b3465, ECK3449

Synonyms: yhhF

Regulation Summary Diagram: ?

Summary:
RsmD is the methyltransferase responsible for methylation of 16S rRNA at the N2 postion of the G966 nucleotide [Lesnyak07]. Its substrate is the 16S ribosomal subunit, but not free unmethylated 16S rRNA [Weitzmann91, Lesnyak07]. RsmD binds 30S ribosomal subunits with rRNA unmodified at G996 tightly [Sergeeva12]. Binding of S7 and S19 together to 16S rRNA allows methylation by RsmD [Weitzmann91]. Methylation of G966 and C967 in 16S rRNA appears to stabilize the binding of initiator tRNA to the 30S pre-initiation complex prior to recognition of the start codon, thus modulating the early stages of translation initiation [Burakovsky12].

A crystal structure of RsmD has been solved at 2.05 Å resolution; the structure shows strong similarity to that of the RsmC methyltransferase [Lesnyak07].

rsmD mutants appear to have no growth defect when grown alone, but have a modest effect on cell fitness in a growth competition assay [Lesnyak07]. Deletion of rsmD alters the initiation frequency from certain translation initiation codons [Arora13].

Review: [Sergiev07]

Locations: cytosol

Map Position: [3,602,416 -> 3,603,012] (77.64 centisomes)
Length: 597 bp / 198 aa

Molecular Weight of Polypeptide: 21.678 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011321 , DIP:DIP-48275N , EchoBASE:EB0339 , EcoGene:EG10343 , EcoliWiki:b3465 , Mint:MINT-1267285 , ModBase:P0ADX9 , OU-Microarray:b3465 , PortEco:rsmD , PR:PRO_000023884 , Pride:P0ADX9 , Protein Model Portal:P0ADX9 , RefSeq:NP_417922 , RegulonDB:EG10343 , SMR:P0ADX9 , String:511145.b3465 , Swiss-Model:P0ADX9 , UniProt:P0ADX9

Relationship Links: InterPro:IN-FAMILY:IPR002052 , InterPro:IN-FAMILY:IPR004398 , PDB:Structure:2FPO , Pfam:IN-FAMILY:PF03602 , Prosite:IN-FAMILY:PS00092

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0070475 - rRNA base methylation Inferred from experiment [Lesnyak07]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0031167 - rRNA methylation Inferred by computational analysis [GOA01a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0052913 - 16S rRNA (guanine(966)-N(2))-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01, Lesnyak07]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rsmD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Credits:
Last-Curated ? 03-Apr-2013 by Keseler I , SRI International


Enzymatic reaction of: 16S rRNA m2G966 methyltransferase

Synonyms: ribosomal RNA small subunit methyltransferase D

EC Number: 2.1.1.171

S-adenosyl-L-methionine + guanine966 in 16S rRNA <=> S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Kinetic Parameters:

Substrate
Km (μM)
Citations
guanine966 in 16S rRNA
0.0033
[Sergeeva12]


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b3465 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10343; confirmed by SwissProt match.


References

Arora13: Arora S, Bhamidimarri SP, Bhattacharyya M, Govindan A, Weber MH, Vishveshwara S, Varshney U (2013). "Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli." Nucleic Acids Res. PMID: 23530111

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Burakovsky12: Burakovsky DE, Prokhorova IV, Sergiev PV, Milon P, Sergeeva OV, Bogdanov AA, Rodnina MV, Dontsova OA (2012). "Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation." Nucleic Acids Res 40(16);7885-95. PMID: 22649054

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lesnyak07: Lesnyak DV, Osipiuk J, Skarina T, Sergiev PV, Bogdanov AA, Edwards A, Savchenko A, Joachimiak A, Dontsova OA (2007). "Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure." J Biol Chem 282(8);5880-7. PMID: 17189261

Sergeeva12: Sergeeva OV, Prokhorova IV, Ordabaev Y, Tsvetkov PO, Sergiev PV, Bogdanov AA, Makarov AA, Dontsova OA (2012). "Properties of small rRNA methyltransferase RsmD: mutational and kinetic study." RNA 18(6);1178-85. PMID: 22535590

Sergiev07: Sergiev PV, Bogdanov AA, Dontsova OA (2007). "Ribosomal RNA guanine-(N2)-methyltransferases and their targets." Nucleic Acids Res 35(7):2295-301. PMID: 17389639

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Weitzmann91: Weitzmann C, Tumminia SJ, Boublik M, Ofengand J (1991). "A paradigm for local conformational control of function in the ribosome: binding of ribosomal protein S19 to Escherichia coli 16S rRNA in the presence of S7 is required for methylation of m2G966 and blocks methylation of m5C967 by their respective methyltransferases." Nucleic Acids Res 19(25);7089-95. PMID: 1766869


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, biocyc13.