4N79

Structure of Cathepsin K-dermatan sulfate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of collagen fiber degradation by cathepsin K.

Aguda, A.H.Panwar, P.Du, X.Nguyen, N.T.Brayer, G.D.Bromme, D.

(2014) Proc.Natl.Acad.Sci.USA 111: 17474-17479

  • DOI: 10.1073/pnas.1414126111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cathepsin K is the major collagenolytic protease in bone that facilitates physiological as well as pathological bone degradation. Despite its key role in bone remodeling and for being a highly sought-after drug target for the treatment of osteoporosi ...

    Cathepsin K is the major collagenolytic protease in bone that facilitates physiological as well as pathological bone degradation. Despite its key role in bone remodeling and for being a highly sought-after drug target for the treatment of osteoporosis, the mechanism of collagen fiber degradation by cathepsin K remained elusive. Here, we report the structure of a collagenolytically active cathepsin K protein dimer. Cathepsin K is organized into elongated C-shaped protease dimers that reveal a putative collagen-binding interface aided by glycosaminoglycans. Molecular modeling of collagen binding to the dimer indicates the participation of nonactive site amino acid residues, Q21 and Q92, in collagen unfolding. Mutations at these sites as well as perturbation of the dimer protein-protein interface completely inhibit cathepsin-K-mediated fiber degradation without affecting the hydrolysis of gelatin or synthetic peptide. Using scanning electron microscopy, we demonstrate the specific binding of cathepsin K at the edge of the fibrillar gap region of collagen fibers, which suggest initial cleavage events at the N- and C-terminal ends of tropocollagen molecules. Edman degradation analysis of collagen fiber degradation products revealed those initial cleavage sites. We propose that one cathepsin K molecule binds to collagen-bound glycosaminoglycans at the gap region and recruits a second protease molecule that provides an unfolding and cleavage mechanism for triple helical collagen. Removal of collagen-associated glycosaminoglycans prevents cathepsin K binding and subsequently fiber hydrolysis. Cathepsin K dimer and glycosaminoglycan binding sites represent novel targeting sites for the development of nonactive site-directed second-generation inhibitors of this important drug target.


    Organizational Affiliation

    Department of Oral Biological and Medical Sciences, Faculty of Dentistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
A
215Homo sapiensMutation(s): 0 
Gene Names: CTSK (CTSO, CTSO2)
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Go to Gene View: CTSK
Go to UniProtKB:  P43235
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IDR
Query on IDR

Download SDF File 
Download CCD File 
A
L-IDURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-VCSGLWQLSA-N
 Ligand Interaction
ASG
Query on ASG

Download SDF File 
Download CCD File 
A
2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
C8 H15 N O9 S
WHCJUIFHMJFEFZ-UIAUGNHASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.830α = 90.00
b = 67.290β = 90.00
c = 90.800γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references