RlmCD belongs to the RFM family of MTases.

<p>(A) The canonical topology diagram of the catalytic domain in the RFM family of MTases. (B) Cartoon representation of the catalytic domain in RlmCD (residue 286–454). SAH is shown as ball-and-stick model. (C) The topology diagram of the catalytic domain in RlmCD. An extra α-helix (α5) is formed at the C-terminus of the catalytic domain.</p

Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD

<div><p>RlmCD has recently been identified as the S-adenosyl methionine (SAM)-dependent methyltransferase responsible for the formation of m⁵U at U747 and U1939 of 23S ribosomal RNA in <i>Streptococcus pneumoniae</i>. In this research, we determine the high-resolution crystal structures of apo-form RlmCD and its complex with SAH. Using an in-vitro methyltransferase assay, we reveal the crucial residues for its catalytic functions. Furthermore, structural comparison between RlmCD and its structural homologue RumA, which only catalyzes the m⁵U1939 in <i>Escherichia coli</i>, implicates that a unique long linker in the central domain of RlmCD is the key factor in determining its substrate selectivity. Its significance in the enzyme activity of RlmCD is further confirmed by in-vitro methyltransferase assay.</p></div

Overall structure of RlmCDs.

<p>(A) Three distinct parts of RlmCDs: the N-terminal TRAM domain, central domain, and C-terminal catalytic domain are colored in blue, green, and orange, respectively. The regions separating the three domains are all colored in grey. (B) The structure superimposition of RlmCDs and RumA (PDB ID 1UWV). RlmCDs and RumA are colored in gray and orange, respectively. (<i>Inset</i>) The superimposition of the central domain is individually shown to highlight the major difference between two structures. (C) The linker A and B of RlmCDs are shown in sticks as well as their electron density map with 2Fo-Fc calculated at 1σ.</p

The 23S rRNA helix 35 is the substrate of RlmCD.

<p>(A) Secondary structures of the 18-mer RNA fragments of the <i>S</i>. <i>pneumoniae</i> (left) and <i>E</i>.<i>coli</i> (right) 23S rRNA helix 35. (B) In-vitro methyltransferase assay of RlmCD. The left three columns represent the methyl transfer activities of the wild-type RlmCD or its mutants toward rRNA-h35. The right three columns represent the methyl transfer activities of the wild-type RlmCD toward the different derivatives of rRNA-h35 (U747A, U747G, and U747C).</p

SAH binds RlmCD at a canonical binding pocket.

<p>(A) The overview of SAH anchored onto the catalytic domain of RlmCD. RlmCD is shown in its electrostatic surface potential, and SAH is shown as ball-and-stick model. (<i>Inset</i>) A close-up of the engagement of SAH into the binding pocket. (B) The interaction details of SAH with RlmCD. RlmCD residues are colored in gray and SAH is colored in green. The gray mesh represents 2Fo-Fc calculated at 1σ density map of SAH and the dashed lines represent the hydrogen bonds.</p

RlmCD is a 23S rRNA methyltransferase.

<p>(A) Comparison of the MTase activities of wild-type RlmCD and its mutants using rRNA-h35 as the substrate. (B) Comparison of the MTase activities of RlmCD toward U747 and U1939. The MTase activity of wild-type RlmCD was normalized to 100%.</p

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-10

<p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>5, hsCBP, hsP/CAF, hsBRG1 and the two components from TAF250. The sequences were aligned based on the experimentally determined three-dimensional structures of these bromodomains, highlighted in green. The secondary structure of Brd2 BD2 is indicated above the alignment. Residues identical in all sequences are shown in red and residues conserved are coloured in blue and residues corresponding to Z sheet (hsBRG1) and helix D are represented in yellow. The two amino acids insertion is indicated by triangle symbols (▼)

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-4

<p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>an value is denoted as a solid line and the mean value plus one standard deviation as a dash line. () A ribbon diagram view mapping the binding interface of H4-AcK12 peptide on Brd2 BD2. The residues, whose combined chemical shift changes were more than the mean value plus one standard deviation and above the mean value, are colored in blue and cyan respectively. The figure B was generated in PyMOL

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-5

<p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>the unacetylated peptide H4-U. Combined chemical shift perturbation was calculated using the equation, , and R = [peptide]/[bromodomain]

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails-8

<p><b>Copyright information:</b></p><p>Taken from "Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails"</p><p>http://www.biomedcentral.com/1472-6807/7/57</p><p>BMC Structural Biology 2007;7():57-57.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2065866.</p><p></p>as a function of residue number of Brd2 BD2. Only those residues of which H-N cross-peaks are resolved enough to permit accurate measurements of their intensities are included