This sharing of binding site in PhBPL which is strikingly different from that observed in EcBirA suggests that catalytic binding sites are organized such that major conformational changes are perhaps not required in group I BPLs during the reaction (22).
The ENCODE database for transcription factor binding sites is organized by institution.
Jenuwein proposed an interesting model in which the distinction between euchromatin and heterochromatin would be given by the way transcription factor binding sites are organized.
As a step towards understanding how individual binding sites are organized on the RRE, how their arrangement relates to the architecture of the Rev oligomer, and how the different sites are recognized by Rev, we solved the structure of a Rev dimer bound to an RRE fragment (IIB40) containing two Rev-binding sites (Daugherty et al., 2008).
However, if the multiple aa-binding sites were organized one by one as shown in Figure 1a, apparently only a few aa-binding sites would be allowed, also due to the stereochemical limitation concerning over-distortion of the RNA's backbone.
The sites are organized into categories like "money management".
First, Rev proteins rapidly bind to a pre-formed region of the RNA molecule where multiple binding sites are compactly organized.
Mammalian transcription factor binding sites are usually organized in clusters that contain several phylogenetically conserved sites for a few different transcription factors [36].
In higher eukaryotes, TF binding sites are often organized in clusters called cis-regulatory modules (CRM) [ 5].
The spliceosome active site is organized around the U5 snRNA loop 1 and the U2/U6 snRNA duplex [ 34], which are involved in binding and correct positioning of the sites of chemistry in the pre-mRNA substrate (5′SS, 3′SS and BP).
The Cildb web site is organized around three main tools, BioMart, NCBI BLAST and GBrowse.
