|Gene:||rsmD||Accession Numbers: EG10343 (EcoCyc), b3465, ECK3449|
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].
|Map Position: [3,602,416 -> 3,603,012] (77.64 centisomes, 280°)||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
|Biological Process:||GO:0070475 - rRNA base methylation
GO:0006364 - rRNA processing [UniProtGOA11a]
GO:0031167 - rRNA methylation [GOA01a]
GO:0032259 - methylation [UniProtGOA11a, GOA01a]
|Molecular Function:||GO:0052913 - 16S rRNA (guanine(966)-N(2))-methyltransferase activity
GO:0003676 - nucleic acid binding [GOA01a]
GO:0008168 - methyltransferase activity [UniProtGOA11a, GOA01a]
GO:0016740 - transferase activity [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09]|
|MultiFun Terms:||information transfer → RNA related → RNA modification|
|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]|
Enzymatic reaction of: 16S rRNA m2G966 methyltransferase
Synonyms: ribosomal RNA small subunit methyltransferase D
EC Number: 188.8.131.52
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.
The reaction is physiologically favored in the direction shown.
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.
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
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
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
©2014 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493