PDBsum entry: 2o97

DNA binding protein

PDB id: 2o97

Contents

Protein chains

70 a.a. *

71 a.a. *

Metals

_CL

_NI

Waters ×26

* Residue conservation analysis

PDB id:

2o97

Name:

DNA binding protein

Title:

Crystal structure of e. Coli hu heterodimer

Structure:

DNA-binding protein hu-alpha. Chain: a. Synonym: ns2, hu-2. Engineered: yes. DNA-binding protein hu-beta. Chain: b. Synonym: ns1, hu-1. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: hupa. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: hupb, hopd.

Resolution:

2.45Å R-factor: 0.228 R-free: 0.264

Authors:

F.Guo,S.Adhya

Key ref:

F.Guo and S.Adhya (2007). Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc Natl Acad Sci U S A, 104, 4309-4314. PubMed id: 17360520 DOI: 10.1073/pnas.0611686104

Date:

13-Dec-06 Release date: 06-Mar-07

Protein chain

P0ACF0  (DBHA_ECOLI) -  DNA-binding protein HU-alpha

Seq: 90 a.a.

Struc: 70 a.a.

Protein chain

P0ACF4  (DBHB_ECOLI) -  DNA-binding protein HU-beta

Seq: 90 a.a.

Struc: 71 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)
• Biological process: chromosome condensation (1 term)
• Biochemical function: protein binding (2 terms)

DOI no: 10.1073/pnas.0611686104

Proc Natl Acad Sci U S A 104:4309-4314 (2007)

PubMed id: 17360520

Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling.

F.Guo, S.Adhya.

ABSTRACT

We determined the crystal structure of the Escherichia coli nucleoid-associated HUalphabeta protein by x-ray diffraction and observed that the heterodimers form multimers with octameric units in three potential arrangements, which may serve specialized roles in different DNA transaction reactions. It is of special importance that one of the structures forms spiral filaments with left-handed rotations. A negatively superhelical DNA can be modeled to wrap around this left-handed HUalphabeta multimer. Whereas the wild-type HU generated negative DNA supercoiling in vitro, an engineered heterodimer with an altered amino acid residue critical for the formation of the left-handed spiral protein in the crystal was defective in the process, thus providing the structural explanation for the classical property of HU to restrain negative supercoils in DNA.

Selected figure(s)

Figure 1.
Fig. 1. Snapshots of electron density maps of residues 12 and 13 as finger prints of the and chains. (a) E12 and K13 of the -subunit. (b) A12 and G13 of . (c) The same region of a with E12 and K13 omitted. The 2F[o] – F[c] map cutoff at 1 is in green. The positive F[o] – F[c] map cutoff at 3 is in red. The red and blue text indicates separate HU dimer molecules.

Figure 7.
Fig. 7. EMSA of HU-DNA. Five nanomolar relaxed plasmid samples were treated with wild-type ^+ ^+ (a) or mutant ^+ -E38A (b) HU at 0, 1.25, 1.39, 1.56, 1.79, 2.08, 2.50, 3.13, 4.17, 6.25, 12.5, 25.0, and 50 µM concentrations (lanes 1–13, respectively).

Figures were selected by an automated process.