PDBsum entry: 1mul

DNA binding protein

PDB id: 1mul

Contents

Protein chain

76 a.a. *

Waters ×50

* Residue conservation analysis

PDB id:

1mul

Name:

DNA binding protein

Title:

Crystal structure of the e. Coli hu alpha2 protein

Structure:

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

Source:

Escherichia coli. Organism_taxid: 562. Gene: hupa. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.234 R-free: 0.267

Authors:

J.Ramstein,N.Hervouet,F.Coste,C.Zelwer,J.Oberto,B.Castaing

Key ref:

J.Ramstein et al. (2003). Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure. J Mol Biol, 331, 101-121. PubMed id: 12875839 DOI: 10.1016/S0022-2836(03)00725-3

Date:

24-Sep-02 Release date: 05-Aug-03

Protein chain

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

Seq: 90 a.a.

Struc: 76 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: 10.1016/S0022-2836(03)00725-3

J Mol Biol 331:101-121 (2003)

PubMed id: 12875839

Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure.

J.Ramstein, N.Hervouet, F.Coste, C.Zelwer, J.Oberto, B.Castaing.

ABSTRACT

The Escherichia coli histone-like HU protein pool is composed of three dimeric forms: two homodimers, EcHUalpha(2) and EcHUbeta(2), and a heterodimer, EcHUalphabeta. The relative abundance of these dimeric forms varies during cell growth and in response to environmental changes, suggesting that each dimer plays different physiological roles. Here, differential scanning calorimetry and circular dichroism (CD) were used to study the thermal stability of the three E.coli HU dimers and show that each of them has its own thermodynamic signature. Unlike the other HU proteins studied so far, which melt through a single step (N(2)<-->2D), this present thermodynamic study shows that the three E.coli dimers melt according to a two-step mechanism (N(2)<-->I(2)<-->2D). The native dimer, N(2), melts partially into a dimeric intermediate, I(2), which in turn yields the unfolded monomers, D. In addition, the crystal structure of the EcHUalpha(2) dimer has been solved. Comparative thermodynamic and structural analysis between EcHUalpha(2) and the HU homodimer from Bacillus stearothermophilus suggests that the E.coli dimer is constituted by two subdomains of different energetic properties. The CD study indicates that the intermediate, I(2), corresponds to an HU dimer having partly lost its alpha-helices. The partially unfolded dimer I(2) is unable to complex with high-affinity, single-stranded break-containing DNA. These structural, thermodynamic and functional results suggest that the N(2)<-->I(2) equilibrium plays a central role in the physiology of E.coli HU. The I(2) molecular species seems to be the EcHUbeta(2) preferential conformation, possibly related to its role in the E.coli cold-shock adaptation. Besides, I(2) might be required in E.coli for the HU chain exchange, which allows the heterodimer formation from homodimers.

Selected figure(s)

Figure 9.
Figure 9. Some structural features of EcHUa[2] homodimer for the protein body partition in two energetic subdomains. A, Structural comparison of the hydrophobic cores of the B. stearothermophilus (BstHU) and the EcHUa[2]. This stereo view shows a superimposition of the aromatic cluster of EcHUa[2] (red) and BstHU (green). The residue 29 of EcHUa[2] and BstHU (Ileu and Phe, respectively) in each dimer are underlined by their side-chains and their van der Waals spheres. B, The N-terminal extremity of BstHU is more anchored at the protein body than that of EcHUa[2]. This stereo view shows the absence in EcHUa[2] (green backbone) of the salt-bridge between Met1' and Asp40 (blue arrow), previously observed in BstHU (pink backbone). In EcHUa[2], this inter-monomer salt-bridge is replaced by an intra-monomer hydrogen bond between the carbonyl group of the Asp40 main-chain and the hydroxyl group of Ser35 side-chain (gray arrow). Hydrogen bonds and salt-bridge are indicated by broken lines (yellow).

Figure 10.
Figure 10. Structural model for the E. coli HU dimer thermal unfolding.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 101-121) copyright 2003.

Figures were selected by an automated process.