PDBsum entry 2f97

Gene regulation

PDB id

2f97

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Contents

			Protein chain

					216 a.a. *

			Ligands

					ACT


					PG4 ×2


					PEG ×2

			Waters ×252

* Residue conservation analysis

PDB id:

2f97

Links

Name:

Gene regulation

Title:

Effector binding domain of benm (crystals generated from high ph conditions)

Structure:

Hth-type transcriptional regulator benm. Chain: a. Synonym: ben and cat operon transcriptional regulator. Engineered: yes

Source:

Acinetobacter baylyi. Organism_taxid: 202950. Strain: adp1. Gene: benm, benr. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å

R-factor:

0.178

R-free:

0.209

Authors:

O.C.Ezezika,S.Haddad,E.L.Neidle,C.Momany

Key ref:

O.C.Ezezika et al. (2007). Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family. Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 361-368. PubMed id: 17565172

Date:

05-Dec-05

Release date:

19-Dec-06

PROCHECK

	Headers

	References

Protein chain

O68014 (BENM_ACIAD) - HTH-type transcriptional regulator BenM from Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

Seq: Struc:					304 a.a. 216 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

	Acta Crystallogr Sect F Struct Biol Cryst Commun 63:361-368 (2007)
PubMed id: 17565172

Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family.
O.C.Ezezika, S.Haddad, E.L.Neidle, C.Momany.

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.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18765907

S.Sainsbury, J.Ren, N.J.Saunders, D.I.Stuart, and R.J.Owens (2008).
Crystallization and preliminary X-ray analysis of CrgA, a LysR-type transcriptional regulator from pathogenic Neisseria meningitidis MC58.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 797-801.

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