Orphan nuclear receptor NGFI-B forms dimers with nonclassical interface

Protein Sci. 2007 Aug;16(8):1762-72. doi: 10.1110/ps.062692207. Epub 2007 Jun 28.

Abstract

The orphan receptor nerve growth factor-induced B (NGFI-B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI-B was shown to be capable of binding both as a monomer to an extended half-site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo- and/or heterodimers. To unveil the structural organization of NGFI-B in solution, we determined the quaternary structure of the NGFI-B LBD by a combination of ab initio procedures from small-angle X-ray scattering (SAXS) data and hydrogen-deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI-B LBD dimer is V-shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI-B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C-terminal fraction of the helix 3. Remarkably, the NGFI-B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI-B and to antagonism of NGFI-B-dependent transcription exercised by GR in cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Circular Dichroism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / isolation & purification
  • Dimerization
  • Mass Spectrometry
  • Models, Biological
  • Models, Molecular
  • Nuclear Receptor Subfamily 4, Group A, Member 1
  • Protein Structure, Secondary
  • Receptors, Cytoplasmic and Nuclear / chemistry*
  • Receptors, Cytoplasmic and Nuclear / genetics
  • Receptors, Cytoplasmic and Nuclear / isolation & purification
  • Receptors, Glucocorticoid / chemistry
  • Receptors, Steroid / chemistry*
  • Receptors, Steroid / genetics
  • Receptors, Steroid / isolation & purification
  • Scattering, Small Angle
  • Solutions
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics
  • Transcription Factors / isolation & purification

Substances

  • DNA-Binding Proteins
  • Nuclear Receptor Subfamily 4, Group A, Member 1
  • Receptors, Cytoplasmic and Nuclear
  • Receptors, Glucocorticoid
  • Receptors, Steroid
  • Solutions
  • Transcription Factors