PDBsum entry: 1hue

DNA-binding

PDB id: 1hue

Contents

Protein chains

90 a.a. *

* Residue conservation analysis

PDB id:

1hue

Name:

DNA-binding

Title:

Histone-like protein

Structure:

Hu protein. Chain: a, b

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422

NMR struc:

25 models

Authors:

H.Vis,M.Mariani,C.E.Vorgias,K.S.Wilson,R.Kaptein,R.Boelens

Key ref:

H.Vis et al. (1995). Solution structure of the HU protein from Bacillus stearothermophilus. J Mol Biol, 254, 692-703. PubMed id: 7500343 DOI: 10.1006/jmbi.1995.0648

Date:

26-May-95 Release date: 15-Oct-95

Protein chains

P0A3H0  (DBH_GEOSE) -  DNA-binding protein HU

Seq: 90 a.a.

Struc: 90 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: chromosome condensation (1 term)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1006/jmbi.1995.0648

J Mol Biol 254:692-703 (1995)

PubMed id: 7500343

Solution structure of the HU protein from Bacillus stearothermophilus.

H.Vis, M.Mariani, C.E.Vorgias, K.S.Wilson, R.Kaptein, R.Boelens.

ABSTRACT

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.

Selected figure(s)

Figure 4.
Figure 4. Ribbon views of HU in two different orthogonal orien- tations. (This pictures were created with the MOLSCRIPT programme (Kraulis, 1991).

Figure 7.
Figure 7. (a) Conformation of the b-hairpin turn of HU. (a) Forty structures of the HU b-hairpin turn (residues 61 to 68) were superimposed on the N, C a and CO atoms of residues 62 to 67. (b) Comparison of the b-hairpin of HU with the first and second iron co-ordinating b-hairpin arms of the iron-sulphur protein rubredoxin from D. vulgaris. (c) Comparison with a 4:6 b-hairpin in the heavy chain of human immunoglobulin fragment Fab New. The conformations of rubredoxin and of Fab New were overlayed on residues 62 to 67 of the b-turn of HU. For the HU b-hairpin turn in (b) and (c) the conformation closest to the average b-turn conformation was used (thin line).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 254, 692-703) copyright 1995.

Figures were selected by an automated process.