PDBsum entry 1hz8

Lipid binding protein

PDB id: 1hz8

Contents

Protein chain

82 a.a. *

Metals

_CA ×2

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Nmr structure and backbone dynamics of a concatemer of epidermal growth factor homology modules of the human low-Density lipoprotein receptor.

Authors

N.D.Kurniawan, K.Aliabadizadeh, I.M.Brereton, P.A.Kroon, R.Smith.

Ref.

J Mol Biol, 2001, 311, 341-356. [DOI no: 10.1006/jmbi.2001.4867]

PubMed id

11478865

Abstract

The ligand-binding region of the low-density lipoprotein (LDL) receptor is formed by seven N-terminal, imperfect, cysteine-rich (LB) modules. This segment is followed by an epidermal growth factor precursor homology domain with two N-terminal, tandem, EGF-like modules that are thought to participate in LDL binding and recycling of the endocytosed receptor to the cell surface. EGF-A and the concatemer, EGF-AB, of these modules were expressed in Escherichia coli. Correct protein folding of EGF-A and the concatemer EGF-AB was achieved in the presence or absence of calcium ions, in contrast to the LB modules, which require them for correct folding. Homonuclear and heteronuclear 1H-15N NMR spectroscopy at 17.6 T was used to determine the three-dimensional structure of the concatemer. Both modules are formed by two pairs of short, anti-parallel beta-strands. In the concatemer, these modules have a fixed relative orientation, stabilized by calcium ion-binding and hydrophobic interactions at the interface. 15N longitudinal and transverse relaxation rates, and [1H]-15N heteronuclear NOEs were used to derive a model-free description of the backbone dynamics of the molecule. The concatemer appears relatively rigid, particularly near the calcium ion-binding site at the module interface, with an average generalized order parameter of 0.85+/-0.11. Some mutations causing familial hypercholesterolemia may now be rationalized. Mutations of D41, D43 and E44 in the EGF-B calcium ion-binding region may affect the stability of the linker and thus the orientation of the tandem modules. The diminutive core also provides little structural stabilization, necessitating the presence of disulfide bonds. The structure and dynamics of EGF-AB contrast with the N-terminal LB modules, which require calcium ions both for folding to form the correct disulfide connectivities and for maintenance of the folded structure, and are connected by highly mobile linking peptides.

Figure 5.
Figure 5. A ribbon diagram showing the secondary structure of EGF-AB. The b-strands are shown with yellow arrows. Two calcium ion sites, located near the N terminus of EGF-A and in the intermodule interface of EGF-AB, are shown with white spheres. The N-terminal EGF-A binding site consists of the carboxyl side-chains of E4 and D18. The aromatic ring of Y23 is involved in calcium binding indirectly by shielding the site from the solvent. The intermodule EGF-AB binding site consists of the backbone carbonyl groups of I42 and L58, the carboxyl side-chains of D41 and E44, and the carbonyl side-chain of N57. The aromatic ring of F31 forms an intermodule interaction with residues E59, G60 and G61 (not labeled for clarity). Y62, which is sequentially equivalent to Y23, is also in close proximity to the calcium ion site but appears not to be involved in the binding. This diagram was produced using Insight98 (Molecular Simulations Inc.).

Figure 8.
Figure 8. (a) Electrostatic surface of EGF-AB, pre- sented in a similar orientation to that in Figure 5. (b) Surface after a 180 ° rotation around the vertical axis in (a). The positively and negatively charged surfaces are shown in blue and red, respectively. These diagrams were produced using Weblab Viewer (Molecular Simu- lations Inc.).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 341-356) copyright 2001.

Secondary reference #1

Title

Nmr structure of a concatemer of the first and second ligand-Binding modules of the human low-Density lipoprotein receptor.

Authors

N.D.Kurniawan, A.R.Atkins, S.Bieri, C.J.Brown, I.M.Brereton, P.A.Kroon, R.Smith.

Ref.

Protein Sci, 2000, 9, 1282-1293. [DOI no: 10.1110/ps.9.7.1282]

PubMed id

10933493

Secondary reference #2

Title

An extracellular beta-Propeller module predicted in lipoprotein and scavenger receptors, Tyrosine kinases, Epidermal growth factor precursor, And extracellular matrix components.

Author

T.A.Springer.

Ref.

J Mol Biol, 1998, 283, 837-862. [DOI no: 10.1006/jmbi.1998.2115]

PubMed id

9790844

Figure 4.
Figure 4. Topology and ribbon diagrams of the six-bladed β-propeller domain predicted for the YWTD domain of nidogen. A, Topology diagram, with each β-sheet given a different color. Sequence repeats are separated by vertical broken lines. Note the offset between sequence repeats and β-sheets. Each sheet is termed a W, with each β-strand representing one leg of the W. β-Strands are represented by arrows. The disulfide bonds in nidogen between strands 2 and 3 of W4 and between the 1-2 loop of W1 and the C-terminal segment in W6 are shown as gold lines. B, Stereo view ribbon representation, with each β-sheet or blade of the nidogen β-propeller model given the same color code as in A. The 4-1 loops that connect each sheet are grey. The view is up the 6-fold pseudosymmetry axis, with the “bottom” of the propeller containing the strand 1 to 2 loops, the strand 3 to 4 loops, and the N and C termini of the propeller domain in the foreground. C, Side view, with the 1-2, 3-4, and N and C termini upward. The side-chain bonds for the cysteine residues in the two disulfide bonds of the nidogen β-propeller domain are shown in gold. The β-strands shown as ribbons are as defined by DSSP [Kabsch and Sander 1983] from the nido model (see Figure 7 and Table 6). Prepared with MOLMOL [Koradi et al 1996].

Figure 6.
Figure 6. Threading scores for YWTD domains. A and B, Average Z-scores for 89 YWTD domains related to LDLR (A) and 18 YWTD domains from sevenless and c-ros (B). Z-scores for each structure were averaged for the 89 or 18 sequences using a program written by Kemin Tan, and plotted with the histogram tool of Microsoft Excel. The arrows mark 1gotB1. C, The distribution of Z-scores for all 107 YWTD domain sequences for the second highest hit, 2aaiB0, ricin β-trefoil domain; and the top hit, 1gotB1, G protein β-propeller domain.

The above figures are reproduced from the cited reference with permission from Elsevier