Abstract of the PDB Structure's related Publication:
The crystal structure of E. coli Fmu, determined at 1.65 A resolution for the apoenzyme and 2.1 A resolution in complex with AdoMet, is the first representative of the 5-methylcytosine RNA methyltransferase family that includes the human nucleolar proliferation-associated protein p120. Fmu contains three subdomains which share structural homology to DNA m(5)C methyltransferases and two RNA binding protein families. In the binary complex, the AdoMet cofactor is positioned within the active site near a novel arrangement of two conserved cysteines that function in cytosine methylation. The site is surrounded by a positively charged cleft large enough to bind its unique target stem loop within 16S rRNA. Docking of this stem loop RNA into the structure followed by molecular mechanics shows that the Fmu structure is consistent with binding to the folded RNA substrate.
RsmB catalyzes the site-specific formation of m5C at position 967 in a loop of hairpin 31 of Domain III in unmodified 16S rRNA transcript. A 16mer mini-substrate encompassing the stem-loop 31 containing the target C967 can also be methylated in vitro, while neither 30S ribosomal subunit nor transcripts of 23S rRNA are substrates for RsmB. AdoMet is the methyl group donor. There is no requirement for Mg. RsmB contains three subdomains which share structural homology to DNA m5C methyltransferases, other AdoMet-dependent methyltransferases and two RNA binding protein families. In Fungi, the homologous gene is Nop2 (RsmB) and in human cell it is the tumor-specific nucleolar proliferation-associated protein P120. RsmB belongs to the same family as E.coli RsmF, yeast Nop2, yeast and archaeal Trm4, Homo sapiens NSUN1 (P120), NSUN2, NSUN3 and NSUN4 (The acronym RsmB has also been used for Regulator of Secondary Metabolism B, a protein not related to RNA small subunit Methyltransferase B).
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.