2F97

Effector Binding Domain of BenM (crystals generated from high pH conditions)

Summary for 2F97

• Entry DOI: 10.2210/pdb2f97/pdb
• Related: 2F6G 2F6P 2F78 2F7A 2F7B 2F7C 2F8D
• Descriptor: HTH-type transcriptional regulator benM, ACETATE ION, TETRAETHYLENE GLYCOL, ... (5 entities in total)
• Functional Keywords: benm, lysr-type regulator, tetramerization, effector binding domain, inducer binding domain, gene regulation
• Biological source: Acinetobacter baylyi
• Total number of polymer chains: 1
• Total formula weight: 27061.18

Authors

Ezezika, O.C.,Haddad, S.,Neidle, E.L.,Momany, C. (deposition date: 2005-12-05, release date: 2006-12-19, Last modification date: 2023-08-30)

Primary citation

Ezezika, O.C.,Haddad, S.,Neidle, E.L.,Momany, C.
Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.
Acta Crystallogr.,Sect.F, 63:361-368, 2007

PubMed Abstract: 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.

PubMed: 17565172
DOI: 10.1107/S1744309107019185

Experimental method

X-RAY DIFFRACTION (2.2 Å)