Post-SET domains

Human Set9 is a 50 kDa H3 methyltransferase that methylates Lys-4 of H3. The enzyme methylated free H3 but not H3 in chromatin substrates. There is evidence that Set9 may stimulate activated transcription [198]. Set9 has the SET domain but lacks the cysteine-rich (pre-SET and post-SET) domains. Disruption of Saccharomyces cerevisiae and Saccharomyces pombe Setl obliterates H3 methyl Lys-4 [199]. Thus this SET domain containing protein appears to be a H3 Lys-4 methyltransferase, catalyzing both di- and tri-methylation of H3 Lys-4 [155]. However, studies with recombinant Setl failed to show histone methyltransferase activity. It has been suggested that other associated proteins may be required for the Setl to be catalytically active [139,200]. Indeed, Setl is associated with several... 

Ashl, a member of the trithorax group of epigenetic activators, methylates H3 at Lys-4 and Lys-9 and H4 at Lys-20. Ashl is a SET domain protein that contains both pre- and post-SET domains [216]. 

The histone methltransferase activity (HMTase) of the SET-domain-containing protein resides within the SET domain. The SET domain itself is approximately 130 amino acids in length (Fig. 4 Jenuwein et al., 1998). Although some areas of the sequence are highly conserved between species, others are much more varied. The pre-SET and post-SET domains can differ in sequence and structure between different HMTases. However, members of the same SET domain protein families have high... 

In a supplementary pathway, links between histone H3 Lys4 methylation and the upregulation of RNA synthesis have also been made. This discrete modification colocalizes with acetylated histone residues and is enriched in the transcriptionally active macronucleus of Tetrahymena [194]. Histone methylation at H3 Lys4 has been recently attributed to the novel HMT SET9, which contains the conserved SET catalytic domain, and noticeably lacks the juxtaposed pre- and post-SET... 

GxG), motif II (YxG), motif III (RFINHxCxPN) and motif IV (ELxFDY where x is any amino acid). The conserved domain folds into several small -sheets that surround a knot-like structure to which additional domains (pre-SET (or nSET), post-SET (or cSET)) or an insertion domain (i-SET) may be added (Figure 2.5). 

As expected the PKS for rapamycin showed a Type I organisation strongly reminiscent of the erythromycin PKS, with catalytic activities arranged in modules (Scheme 27) and with sets of modules housed in turn in three multi-modular cassettes designated RAPS 1, RAPS 2 and RAPS 3. RAPS 1 contains modules 1 to 4, RAPS 2 modules 5 to 10, and RAPS 3 modules 11 to 14. The domain structure of the rapamycin PKS may not correspond in every detail to the pattern expected from the proposed structure for the PKS product however. In modules 3 and 6, there appear to be potentially active KR and DH domains which are not required module 3 also contains a potentially active but functionally redundant ER domain. It is possible that the active sites of these extra domains have been inactivated in a way that is not apparent from the primary sequence, and that the now redundant protein residues have still to be edited out by the random processes of evolution. There is also a chance that all these domains are indeed active and that the true rapamycin PKS product is more fully reduced than that shown. Extra post-PKS reoxidations would then be required to reintroduce the oxygen functionality at the relevant sites in the final structure. 

An enormous range of medically important polyketide and peptide natural products assembled by modular polyketide synthases (PKSs), non-ribosomal peptide synthases (NRPSs) and mixed PKS/NRPS systems have macrocyclic structures, including the antibiotics erythromycin (PKS) and daptomycin (NRPS), the immunosuppressants cyclosporin (NRPS) and rapamycin (PKS/NRPS), and the antitumor agent epothilone (PKS/NRPS). PKSs and NRPSs are large, multifunctional proteins that are organized into sets of fnnc-tional domains termed modules. The order of modules corresponds directly to the seqnence of monomers in the product. Synthetic intermediates are covalently tethered by thioester linkages to a carrier protein domain in each module. The thiol tether on each carrier domain is phosphopantetheine, which is attached to a conserved serine residne in the carrier protein in a post-translational priming reaction catalyzed by a phosphopantetheinyltransferase. 

Execution of the method requires the physical domain to be divided into a distribution of conqiutational cells. The cells provide geometric boundaries and volumes, which are used to sample macroscopic properties. Also, only molecules located within the same cell, at a given time, are allowed to collide. The DSMC simulation proceeds from a set of prescribed initial condition. The molecules randomly populate the computational domain. These simulated molecules are assigned random velocities, usually based on the equilibrium distribution. The simulated representative particles move for a certain time step. This molecule motion is modeled deterministically. This process enforces the boundary conditions. With the simulated particles being appropriately indexed, the molecular collision process can be performed. The collision process is modeled statistically, which is different from deterministic simulation methods such as the molecular dynamics methods. In general, only particles within the same computational cell are considered to be possible collision partners. Mthin each cell, collision pairs are selected randomly and a representative set of collisions is performed. The post-collision velocities are determined. There are several... 

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