Taxonomic distribution of proteins containing BHL domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing BHL domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Transcription factors 1: bZIP proteins.

Hurst HC
Protein Profile. 1995; 2: 101-68

Solution structure of the HU protein from Bacillus stearothermophilus.

Vis H, Mariani M, Vorgias CE, Wilson KS, Kaptein R, Boelens R
J Mol Biol. 1995; 254: 692-703

The histone-like protein HU from Bacillus stearothermophilus is a dimer with a molecular mass of 19.5 kDa that is capable of bending DNA. An X-ray structure has been determined, but no structure could be established for a large part of the supposed DNA-binding beta-arms. Using distance and dihedral constraints derived from triple-resonance NMR data of a 13C/15N doubly-labelled HU protein 49 distance geometry structures were calculated, which were refined by means of restrained Molecular Dynamics. From this set a total of 25 refined structures were selected having low constraint energy and few constraint violations. The ensemble of 25 structures display a root-mea-square co-ordinate deviation of 0.36 A with respect to the average structure, calculated over the backbone heavy atoms of residues 2 to 54 and 75 to 90 (and residues 2' to 54' and 75' to 90' of the second monomer). The structure of the core is very similar to that observed in the X-ray structure, with a pairwise r.m.s.d. of 1.06 A. The structure of the beta-hairpin arm contains a double flip-over at the prolines in the two strands of the beta-arm. Strong 15N-NH heteronuclear nuclear Overhauser effects indicate that the beta-arm and especially the tip is flexible. This explains the disorder observed in the solution and X-ray structures of the beta-arm, in respect of the core of the protein. Overlayed onto itself the beta-arm is better defined, with an r.m.s.d. of 1.0 A calculated over the backbone heavy atoms of residues 54 to 59 and 69 to 74. The tip of the arm adopts a well-defined 4:6 beta-hairpin conformation similar to the iron co-ordinating beta-arms of rubredoxin.

Homeodomain-DNA recognition.

Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wuthrich K
Cell. 1994; 78: 211-23

The MerR metalloregulatory protein binds mercuric ion as a tricoordinate, metal-bridged dimer.

Helmann JD, Ballard BT, Walsh CT
Science. 1990; 247: 946-8

Bacterial MerR proteins are dimeric DNA-binding proteins that mediate the Hg(II)-dependent induction of mercury resistance operons. Site-directed mutagenesis of the Bacillus sp. RC607 MerR protein reveals that three of four Cys residues per monomer are required for Hg(II) binding at the single high-affinity binding site. Inactive mutant homodimers can exchange subunits to form heterodimers active for Hg(II) binding. Studies of a heterodimer retaining only three of eight cysteine residues per dimer reveal that Cys79 in one subunit and Cys114 and Cys123 in the second subunit are necessary and sufficient for high-affinity Hg(II) binding in an asymmetric, subunit bridging coordination complex.

Histonelike proteins of bacteria.

Drlica K, Rouviere-Yaniv J
Microbiol Rev. 1987; 51: 301-19

3-A resolution structure of a protein with histone-like properties in prokaryotes.

Tanaka I, Appelt K, Dijk J, White SW, Wilson KS
Nature. 1984; 310: 376-81

The 3-A structure of DNA-binding protein II, which exhibits histone-like properties in bacteria, has been determined. The molecule is dimeric and appears to bind to the phosphate backbone of DNA through two symmetry-related arms. A mechanism by which the protein induces DNA supercoiling is proposed.