PDBsum entry 1m7c

RNA binding protein

PDB id: 1m7c

Contents

Protein chains

(+ 0 more) 68 a.a.

Theoretical model

PDB id:

1m7c

Name:

RNA binding protein

Title:

Stuctural model of e. Coli hfq

Structure:

Hfq protein. Chain: a, b, c, d, e, f. Fragment: sm-like n-terminal region

Source:

Escherichia coli. Bacteria

Authors:

V.Arluison,P.Derreumaux,F.Allemand,M.Folichon,E.Hajnsdorf, P.Regnier

Key ref:

V.Arluison et al. (2002). Structural Modelling of the Sm-like Protein Hfq from Escherichia coli. J Mol Biol, 320, 705-712. PubMed id: 12095248 DOI: 10.1016/S0022-2836(02)00548-X

Date:

19-Jul-02 Release date: 07-Aug-02

Protein chains

P25521  (HFQ_ECOLI) -

DOI no: 10.1016/S0022-2836(02)00548-X

J Mol Biol 320:705-712 (2002)

PubMed id: 12095248

Structural Modelling of the Sm-like Protein Hfq from Escherichia coli.

V.Arluison, P.Derreumaux, F.Allemand, M.Folichon, E.Hajnsdorf, P.Régnier.

ABSTRACT

The Hfq polypeptide of Escherichia coli is a nucleic acid-binding protein involved in the expression of many proteins. Derivation of its three-dimensional structure is important for our understanding of its role in gene regulation at the molecular level. In this study, we combined computational and biophysical analysis to derive a possible structure for Hfq. As a first step towards determining the structure, we searched for possible sequence-structure compatibility, using secondary structure prediction and protein domain and fold-recognition methods available on the WEB. One fold, essentially beta sheet in character, the Sm motif of small nuclear ribonucleoproteins, even though it initially fell well below the confidence thresholds, was proposed and further validated by a series of biophysical and biochemical studies. The Hfq hexamer structure was modelled on the human Sm D3B structure using optimised sequence alignments and molecular mechanics methods. This structure accounts for the physico-chemical properties of Hfq and highlights amino acid residues that could interact with RNA.

Selected figure(s)

Figure 2.
Figure 2. The multiple sequence alignment of E. coli Hfq with SMART00651 protein domains along with the location of the Sm1 and Sm2 subdomains, the linker segments, and the b strands within known protein structures. (a) Alignment between Hfq and the SMART domain of Sm proteins. (b) Combination of the multiple sequence alignment and the secondary structure predictions. Residues of Hfq predicted to be in a helix and b strands by the two predictive methods (Figure 1) are underlined by straight and wavy lines, respectively. Stretches of amino acid residues of Sm proteins in a helix and b strands are indicated by h1 and b1, b2, b3, b4 and b5, respectively, and delimited by hyphens. Positions that are conserved in most Sm are highlighted in grey and those conserved in Sm and Hfq are highlighted in black. Residues participating in the base-binding pocket of the archael AF-Sm1 [26] and equivalent amino acid residues in Hfq are labelled with a star. Lowercase in the human Sm D2 (1B34b) sequence refers to residues that are disordered in the crystal structure and for which there are no coordinates. The a carbon atoms of the Met73 and Asp93 framing this disordered segment are 5.3 Å apart.[16]

Figure 3.
Figure 3. The generated Hfq model. The SWISS-MODEL server[49] was used to generate the structure of the Hfq monomeric form. Since automated construction requires 30% identity between the query and target sequences, the determined X-ray structure of human Sm D3-B (PDB entry 1D3B) [16] was used with its amino acid sequences mutated according to the alignments ( Figure 2(b)). The model was then the subject of EEF1 energy minimisation. [50] The EEF1 energy model combines the CHARMM19 polar hydrogen potential energy function and a simple Gaussian model for the solvation free energy. [50] The resulting structure was used as a template for generating the complex following the symmetry operations of the human Sm 1D3B crystal. The hexamer was minimised for 1500 steps using the EEF1 energy model and the resulting structure satisfied all PROCHECK stereochemical verifications. [51] (a) Structure of the E. coli Hfq hexamer. The molecules are shown as ribbons of different colours showing a helix and b strand. (b) Dimer contacts in the Hfq hexamer: the b4 strand in one monomer interacts with the b5 strand of a neighbouring subunit. (c) Left, the Hfq putative base-binding pocket with the conserved residues Phe42 and Lys56; right, X-ray structure of the base-binding pocket within the RNA-Af-Sm1 complex.[26] The Figures were produced with the RASMOL software package. [52] (d) Electrostatic surface charge potential showing the two faces of the six ring-shaped structure. The left picture corresponding to the top view shown in (a) emphasises the positively charged cavity of the ring as indicated by the blue colour. The right picture points to the continuously positive surface potential of the other side. The Figure was produced by GRASP. [53]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 705-712) copyright 2002.

Figures were selected by an automated process.