2F8D: Benm Effector-binding Domain Crystallized From High Ph Conditions

LysR-type transcriptional regulators comprise the largest family of homologous regulatory DNA-binding proteins in bacteria. A problematic challenge in the crystallization of LysR-type regulators stems from the insolubility and precipitation difficulties encountered with high concentrations of the full-length versions of these proteins. A general oligomerization scheme is proposed for this protein family based on the structures of the effector-binding domain of BenM in two different space groups, P4(3)22 and C222(1). These structures used the same oligomerization scheme of dimer-dimer interactions as another LysR-type regulator, CbnR, the full-length structure of which is available [Muraoka et al. (2003), J. Mol. Biol. 328, 555-566]. Evaluation of packing relationships and surface features suggests that BenM can form infinite oligomeric arrays in crystals through these dimer-dimer interactions. By extrapolation to the liquid phase, such dimer-dimer interactions may contribute to the significant difficulty in crystallizing full-length members of this family. The oligomerization of dimeric units to form biologically important tetramers appears to leave unsatisfied oligomerization sites. Under conditions that favor association, such as neutral pH and concentrations appropriate for crystallization, higher order oligomerization could cause solubility problems with purified proteins. A detailed model by which BenM and other LysR-type transcriptional regulators may form these arrays is proposed.
PDB ID: 2F8DDownload
MMDB ID: 43278
PDB Deposition Date: 2005/12/2
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Similar Structures:
Biological Unit for 2F8D: dimeric; determined by author and by software (PISA)
Molecular Components in 2F8D
Label Count Molecule
Proteins (2 molecules)
Hth-type Transcriptional Regulator Benm(Gene symbol: BEN76_RS06785)
Molecule annotation
Chemicals (10 molecules)
* Click molecule labels to explore molecular sequence information.

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