Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan

Abstract

Decorin is a ubiquitous extracellular matrix proteoglycan with a variety of important biological functions that are mediated by its interactions with extracellular matrix proteins, cytokines, and cell surface receptors. Decorin is the prototype of the family of small leucine-rich repeat proteoglycans and proteins (SLRPs), characterized by a protein core composed of leucine-rich repeats (LRRs), flanked by two cysteine-rich regions. We report here the crystal structure of the dimeric protein core of decorin, the best characterized member of the SLRP family. Each monomer adopts the curved solenoid fold characteristic of LRR domains, with a parallel beta-sheet on the inside interwoven with loops containing short segments of beta-strands, 3(10) helices, and polyproline II helices on the outside. Two main features are unique to this structure. First, decorin dimerizes through the concave surfaces of the LRR domains, which have been implicated previously in protein-ligand interactions. The amount of surface buried in this dimer rivals the buried surfaces of some of the highest-affinity macromolecular complexes reported to date. Second, the C-terminal region adopts an unusual capping motif that involves a laterally extended LRR and a disulfide bond. This motif seems to be unique to SLRPs and has not been observed in any other LRR protein structure to date. Possible implications of these features for decorin ligand binding and SLRP function are discussed.

Fig. 1.

Structure of the LRR domain of bovine decorin. (a) Ribbon diagram of the dimeric structure of decorin LRR domain. Green arrows, β-strands; red ribbons, α-helical turns; pink tubes, segments of polyproline II helix; orange ribbons, short segments of 3₁₀ helices and β-turns; yellow sticks, disulfide bonds. (b) Internal organization of bovine decorin LRRs (residues 22-326). Yellow highlight, LRR consensus residues; red highlight, Cys residues; green highlight, consensus residues for the 24-aa repeat; cyan highlight, consensus residues for the 21-aa repeat; blue highlight, Asn residues with oligosaccharide substituents; red boxes, amino acids that contribute to β-sheets.

Fig. 2.

Topology and secondary structure of the C-terminal capping motif. (a) Ribbon diagram of the C-terminal capping motif of decorin. This motif includes LRR-XI, LRR-XII, and the additional C-terminal strand β13. Secondary structural elements are depicted as in Fig. 1. (b) Rope diagram of a glycosylated, extended model of the decorin dimer, showing the position of the two ear repeats (blue arrows). Extended oligosaccharide chains have been modeled (gray) onto the three N-acetylglucosamine residues (blue) to illustrate their approximate size and general positioning relative to the dimer surface. Both N termini also have been extended a few residues (gray) to illustrate the general sense of directionality. The GAG chains are not included in the model. (c) Structure-based alignment for the C-terminal motifs. Green text, class I SLRPs; red text, class II SLRPs; blue text, class III SLRPs. Yellow, conserved residues; red, conserved Cys residues; green, partially conserved residues; cyan, partially conserved Pro residues indicative of polyproline II conformation; magenta, polar residues occupying hallmark LRR hydrophobic sites. The blue double-headed arrow indicates the extent of the ear. Ear repeats in keratocan and PRELP are significantly longer than those for all other SLRPs and, therefore, are shown as containing insertion loops. The decorin sequence is that of the bovine protein; all others are of human proteins.

Fig. 3.

Extent and sequence conservation of the dimer interface. (a) View of the concave side of a decorin monomer. Residues that are buried from solvent in the dimer are shown in orange. (b) Two-dimensional representation of the surface residues at the concave side of class I SLRPs. Yellow, residues fully conserved in all three SLRPs; green, partially conserved residues; black outline, the footprint of the decorin dimerization interface. The relative positions and directions of the 14 β-strands that form the concave side β-sheet are indicated.

Fig. 4.

Molecular interactions at the dimer interface. (a) The aromatic ring of Phe-27 in one monomer (green) becomes intercalated between the aromatic rings of two His residues in the other monomer (red). This hydrophobic sandwich is part of an extended hydrophobic array (see text). (b) Extensive hydrogen-bonding networks (blue dotted lines) occur between the two monomers.