Overview of NuRISITE

NuRISITE (Nuclear Receptor Interaction Site)
is a database for identifying the interaction
sites in 3D structures of nuclear receptors,
and for providing detailed information on the
interactions between nuclear receptors (NRs)
and their partners. These include (1) the
interactions of residues in the ligand binding
domains (LBDs) with various ligands
(agonists, partial agonists and antagonists),
as well as coregulators (i.e., coactivators,
corepressors, or their fragments), and (2) the
interactions of residues in the DNA-binding
domains (DBDs) with response elements.
 

The unified nomenclature system for the nuclear receptor superfamily was
used to divide nuclear receptors into 5 subfamilies and 24 groups. For each
group, the protein sequences of all the published PDB structures were
aligned to the pre-selected representative sequence of the cluster. The
pairwise alignments within the cluster were stacked upon each other to
generate a multiple alignment of all sequences relative to the
representative. Interactions between protein and ligand atoms are
extracted from each NR structure in the PDB. Based on the alignments and
the interactions found for individual NRs, consensus interaction sites were
constructed for both the LBD and the DBD of the each NR group, providing
information on the amino acid positions that are in contact with any ligand
within the particular subfamily of receptors.

Given a PDB id, a SWISS_PROT id, or a NCBI accession number for a nuclear
receptor, NuRISITE permits the user to determine the interaction sites for
the query, and to display the amino acid residues of the consensus
interaction site for the relevant subfamily. Given an arbitrary protein
sequence, NuRISITE can also be used to identify the subfamily, if any, of
nuclear receptors to which the query most likely belongs, and then to
predict putative interaction sites based on the alignment with the
appropriate sequence.