PDBsum entry: 1kdk

Transport protein

PDB id: 1kdk

Contents

Protein chain

177 a.a. *

Ligands

DHT

Waters ×89

* Residue conservation analysis

PDB id:

1kdk

Name:

Transport protein

Title:

The structure of the n-terminal lg domain of shbg in crystals soaked with edta

Structure:

Sex hormone-binding globulin. Chain: a. Fragment: n-terminal lg-domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.70Å R-factor: 0.194 R-free: 0.245

Authors:

I.Grishkovskaya,G.V.Avvakumov,G.L.Hammond,Y.A.Muller

Key ref:

I.Grishkovskaya et al. (2002). Resolution of a disordered region at the entrance of the human sex hormone-binding globulin steroid-binding site. J Mol Biol, 318, 621-626. PubMed id: 12054810 DOI: 10.1016/S0022-2836(02)00169-9

Date:

13-Nov-01 Release date: 15-May-02

Protein chain

P04278  (SHBG_HUMAN) -  Sex hormone-binding globulin

Seq: 402 a.a.

Struc: 177 a.a.

DOI no: 10.1016/S0022-2836(02)00169-9

J Mol Biol 318:621-626 (2002)

PubMed id: 12054810

Resolution of a disordered region at the entrance of the human sex hormone-binding globulin steroid-binding site.

I.Grishkovskaya, G.V.Avvakumov, G.L.Hammond, Y.A.Muller.

ABSTRACT

The crystal structure of human sex hormone-binding globulin (SHBG) has revealed how 5alpha-dihydrotestosterone intercalates between the two seven-stranded beta-sheets of its amino-terminal laminin G-like domain. However, a region of disorder (residues 130 to 135 of SHBG) was identified together with a zinc-binding site in immediate proximity to the steroid. It has been important to resolve the structure of this region because previous studies have suggested that these residues may contribute to steroid binding directly. Here, we present the 2.35 A and 1.7 A crystal structures of the amino-terminal LG domain of SHBG obtained from a tetragonal crystal form and by EDTA-soaking of a trigonal crystal form, respectively. In both of these new structures, residues Pro130 to Arg135 are now clearly visible. Substitution of the two residues (Leu131Gly and Lys134Ala) pointing towards the steroid has shown that only Leu131 contributes significantly to steroid binding. Rather than covering the steroid-binding pocket in an extended conformation, a 3(10) helical turn is formed by residues Leu131 to Lys134 in this segment. Unfolding of this secondary structure element can either facilitate the entry of the steroids into the binding site or modulate the important contribution that Leu131 makes to steroid binding. A comparison with previous structures supports the concept that zinc binding re-orients the side-chain of His136, and this residue serves as a lever causing disorder within the loop structure between Pro130 and Arg135.

Selected figure(s)

Figure 1.
Figure 1. Comparison of the SHBG steroid-binding site structure in the presence or in the absence of zinc. (a) The s[a]-weighted 2F[o] -F[c] electron density for the loop segment 130 to 137 in the tetragonal crystal form calculated at 2.35 Å resolution and contoured at 0.9s. Only electron density within 2.5 Å of the displayed atoms is shown. (b) Stereorepresentation of the steroid-binding site of SHBG in the EDTA-soaked crystals obtained at 1.7 Å resolution. The loop segment 130 to 135 is clearly visible and adopts a 3[10] helical turn characterized by a main-chain to main-chain hydrogen bond between Leu131 and Lys134. The side-chain of Lys134 makes a hydrogen bond to the 17b-hydroxy group of DHT. The steroid is shown in a ball and stick representation (yellow and green). Protein main-chain discontinuities are indicated by black spheres. (c) Stereorepresentation of the steroid-binding site of SHBG obtained previously with trigonal crystals in the presence of zinc (PDB accession code 1F5F). Zinc does not bind to a preformed binding site, and zinc binding causes the reorientation of the side-chains of residues Asp65, His83 and His136. As a result, we propose that the reorientation of residue His136 causes disorder of the loop segment (broken line). The Figure was prepared with MOLSCRIPT[13.] and Raster3d. [14.]

The above figure is reprinted by permission from Elsevier: J Mol Biol (2002, 318, 621-626) copyright 2002.