PDBsum entry 1xec

Structural protein

PDB id: 1xec

Contents

Protein chains

305 a.a. *

Ligands

NAG-NAG ×2

NAG ×3

Waters ×298

* Residue conservation analysis

PDB id:

1xec

Name:

Structural protein

Title:

Dimeric bovine tissue-extracted decorin, crystal form 2

Structure:

Decorin. Chain: a, b. Synonym: bone proteoglycan ii. Pg-s2

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: skin. Other_details: protein was extracted from calf skin under denaturing conditions and refolded

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.214 R-free: 0.263

Authors:

P.G.Scott,P.A.Mcewan,C.M.Dodd,E.M.Bergmann,P.N.Bishop,J.Bella

Key ref:

P.G.Scott et al. (2004). Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan. Proc Natl Acad Sci U S A, 101, 15633-15638. PubMed id: 15501918 DOI: 10.1073/pnas.0402976101

Date:

09-Sep-04 Release date: 02-Nov-04

Protein chains

P21793  (PGS2_BOVIN) -  Decorin from Bos taurus

Seq: 360 a.a.

Struc: 305 a.a.

DOI no: 10.1073/pnas.0402976101

Proc Natl Acad Sci U S A 101:15633-15638 (2004)

PubMed id: 15501918

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

P.G.Scott, P.A.McEwan, C.M.Dodd, E.M.Bergmann, P.N.Bishop, J.Bella.

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.

Selected figure(s)

Figure 3.
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 -strands that form the concave side -sheet are indicated.

Figure 4.
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.

Figures were selected by an automated process.