PDBsum entry 1kqw

Transport protein

PDB id: 1kqw

Contents

Protein chain

134 a.a. *

Ligands

RTL

Waters ×194

* Residue conservation analysis

PDB id:

1kqw

Name:

Transport protein

Title:

Crystal structure of holo-crbp from zebrafish

Structure:

Cellular retinol-binding protein. Chain: a. Synonym: crbp. Engineered: yes

Source:

Danio rerio. Zebrafish. Organism_taxid: 7955. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.38Å R-factor: 0.165 R-free: 0.243

Authors:

V.Calderone,C.Folli,A.Marchesani,R.Berni,G.Zanotti

Key ref:

V.Calderone et al. (2002). Identification and structural analysis of a zebrafish apo and holo cellular retinol-binding protein. J Mol Biol, 321, 527-535. PubMed id: 12162964 DOI: 10.1016/S0022-2836(02)00628-9

Date:

08-Jan-02 Release date: 28-Aug-02

Protein chain

Q8UVG6  (Q8UVG6_DANRE) -  Cellular retinol-binding protein type II from Danio rerio

Seq: 135 a.a.

Struc: 134 a.a.

DOI no: 10.1016/S0022-2836(02)00628-9

J Mol Biol 321:527-535 (2002)

PubMed id: 12162964

Identification and structural analysis of a zebrafish apo and holo cellular retinol-binding protein.

V.Calderone, C.Folli, A.Marchesani, R.Berni, G.Zanotti.

ABSTRACT

Cellular retinol-binding proteins (CRBPs) are cytoplasmic retinol-specific binding proteins. Mammalian CRBPs have been thoroughly characterised previously. Here we report on the identification and X-ray structural analysis of the apo (1.7A resolution) and holo (1.4A resolution) forms of a zebrafish CRBP. According to amino acid sequence and structure analyses, the zebrafish CRBP that we have identified resembles closely mammalian CRBP II, suggesting that it is the zebrafish orthologue of this mammalian CRBP type. Zebrafish CRBP forms a tight complex with all-trans retinol, producing an absorption spectrum similar to those of mammalian holo-CRBPs, albeit slightly blue-shifted. The superposition of the alpha-carbon atoms of the liganded (complexed with retinol) and unliganded forms of zebrafish CRBP shows significant differences in correspondence of the betaC-betaD (residues 55-58) and betaE-betaF (residues 74-77) turns, providing evidence for the occurrence of conformational changes accompanying retinol binding/release. Remarkable and well-defined ligand-dependent conformational changes in the protein region comprising the two beta-turns affect both the main chain and the side-chains of several residues. The two beta-turns project towards the interior of the cavity devoid of ligand of the apoprotein. The side-chains of F57, Y60 and L77 change substantially their orientation and position in the apoprotein relative to the holoprotein. In the beta-barrel internal cavity of apo-CRBP they occupy some of the space that is otherwise occupied by bound retinol in holo-CRBP, and are displaced from these positions on ligand binding. These results indicate that a flexible area encompassing the betaC-betaD and betaE-betaF turns may serve as the ligand portal and that these turns undergo conformational changes associated with the not yet clarified mechanism of retinol binding and release in CRBPs.

Selected figure(s)

Figure 3.
Figure 3. (a) Ribbon drawing of the molecular model of zebrafish CRBP. The barrel forming b-strands (from A to J) and the two a-helices (I and II) are shown. The CRBP-bound retinol molecule (ball/stick model), within the b-barrel internal cavity, is also shown. (b) Stereo view showing the superposition of the a-carbon chain traces of zebrafish holo-CRBP (red coloured), rat holo-CRBP I (green coloured, PDB ID Code 1CRB) and rat holo-CRBP II (violet colored, PDB ID Code 1OBP). CRBP-bound retinol molecules (ball/stick model) are represented with the same color of the corresponding protein. (c) Portion of the electron density map around the ligand and some neighbouring residues within the b-barrel internal cavity of zebrafish holo-CRBP. The map is calculated with coefficients |2F[obs] -F[calc]| and contoured at 1.3 b. Broken lines (green coloured) indicate two possible hydrogen bond interactions established by the retinol hydroxyl group (see the text for details) with the side-chains of Q108 and T51.

Figure 4.
Figure 4. Superposition of the zebrafish holo and apo-CRBP structures. (a) Stereo view of the a-carbon chain trace of zebrafish holo-CRBP (green colored) superimposed on that of the apoprotein (red coloured). The most significant conformational changes affect the region of the bC-bD (residues 55-58) and bE-bF (residues 74-77) turns. (b) Enlarged stereo view showing the differences in conformation and/or position of the side-chains of residues F57, R58, Y60 and L77 for the apo and holo forms of zebrafish CRBP (holoprotein, green colored; apoprotein, red coloured). The CRBP-bound retinol molecule (ball/stick model) is also shown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 321, 527-535) copyright 2002.

Figures were selected by an automated process.