1. NUCLEAR RECEPTORS NOMENCLATURE COMMITTEE
A unified nomenclature system for the nuclear receptor superfamily.
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2. NISHIKAWA, J-I., KITAURA, M., IMAGAWA, M. AND NISHIHARA, T.
Vitamin D receptor contains multiple dimerisation interfaces that
are functionally different.
NUCLEIC ACIDS RES. 23(4) 606-611 (1995).
3. DE VOS, P., SCHMITT, J., VERHOEVEN, G. AND STUNNENBERG, G.
Human androgen receptor expressed in HeLa cells activates transcription
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4. WAGNER, R.L., APRILETTI, J.W., MCGRATH, M.E., WEST, B.L., BAXTER, J.D.
AND FLETTERICK, R.J.
A structural role for hormone in the thyroid hormone receptor.
NATURE 378 690-697 (1995).
5. CHEN, J.D. AND EVANS, R.M.
A transcriptional co-repressor that interacts with nuclear hormone
NATURE 377 454-457 (1995).
Steroid or nuclear hormone receptors (NRs) constitute an important super-
family of transcription regulators that are involved in widely diverse
physiological functions, including control of embryonic development, cell
differentiation and homeostasis . Members of the superfamily include the
steroid hormone receptors and receptors for thyroid hormone, retinoids,
1,25-dihydroxy-vitamin D3 and a variety of other ligands. The proteins
function as dimeric molecules in nuclei to regulate the transcription of
target genes in a ligand-responsive manner [1,2]. In addition to C-terminal
ligand-binding domains, these nuclear receptors contain a highly-conserved,
N-terminal zinc-finger that mediates specific binding to target DNA
sequences, termed ligand-responsive elements. In the absence of ligand,
steroid hormone receptors are thought to be weakly associated with nuclear
components; hormone binding greatly increases receptor affinity.
NRs are extremely important in medical research, a large number of them
being implicated in diseases such as cancer, diabetes, hormone resistance
syndromes, etc. . While several NRs act as ligand-inducible transcription
factors, many do not yet have a defined ligand and are accordingly termed
"orphan" receptors. During the last decade, more than 300 NRs have been
described, many of which are orphans, which cannot easily be named due to
current nomenclature confusions in the literature. However, a new system
has recently been introduced in an attempt to rationalise the increasingly
complex set of names used to describe superfamily members .
In common with other members of the steroid hormone receptor family, thyroid
hormone receptors (TRs) contain 2 major highly-conserved domains, involved
in DNA- and ligand-binding respectively. Except for a conserved 12-residue
motif adjacent to the DNA-binding domain, the N-terminal domains are
divergent between alpha- and beta-TR isoforms (but are conserved within
isoforms). The DNA-binding domain is the most highly conserved feature of
the family; it contains 2 zinc-binding modules (zinc fingers). The ligand-
binding domain  includes a number of conserved motifs, parts of which
are thought to be involved in dimerisation. The hinge region between these
2 domains  is thought to contain the binding site for transcriptional
co-repressor proteins that mediate the transcriptional repression function
of unliganded receptors: for more information see the TRR resource at
THYROIDHORMR is a 9-element fingerprint that provides a signature for the
thyroid hormone receptors. The fingerprint was derived from an initial
alignment of 17 sequences: the motifs were drawn from conserved regions
spanning virtually the full alignment length, focusing on those areas of
the alignment that characterise the TRs but distinguish them from the
rest of the steroid hormone receptor family - motif 1 lies at the
N-terminus just prior to the DNA-binding domain; and motifs 2-9 span the
hinge and ligand-binding regions. Two iterations on OWL28.0 were required
to reach convergence, at which point a true set comprising 40 sequences
was identified. Three partial matches were also found (RATERBAA2, JC4014
and MMU9419), all of which are steroid hormone receptor family members.
An update on SPTR37_9f identified a true set of 29 sequences, and 1