3H7D

The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.242 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-activity analysis of cathepsin K/chondroitin 4-sulfate interactions.

Cherney, M.M.Lecaille, F.Kienitz, M.Nallaseth, F.S.Li, Z.James, M.N.Bromme, D.

(2011) J.Biol.Chem. 286: 8988-8998

  • DOI: 10.1074/jbc.M110.126706

  • PubMed Abstract: 
  • In the presence of oligomeric chondroitin 4-sulfate (C4-S), cathepsin K (catK) forms a specific complex that was shown to be the source of the major collagenolytic activity in bone osteoclasts. C4-S forms multiple contacts with amino acid residues on ...

    In the presence of oligomeric chondroitin 4-sulfate (C4-S), cathepsin K (catK) forms a specific complex that was shown to be the source of the major collagenolytic activity in bone osteoclasts. C4-S forms multiple contacts with amino acid residues on the backside of the catK molecule that help to facilitate complex formation. As cathepsin L does not exhibit a significant collagenase activity in the presence or in the absence of C4-S, we substituted the C4-S interacting residues in catK with those of cathepsin L. Variants revealed altered collagenolytic activities with the largest inhibitory effect shown by the hexavariant M5. None of the variants showed a reduction in their gelatinolytic and peptidolytic activities when compared with wild-type catK, indicating no structural alteration within their active sites. However, the crystal structure of the M5 variant in the presence of oligomeric C4-S revealed a different binding of chondroitin 4-sulfate. C4-S is not continuously ordered as it is in the wild-type catK┬ĚC4-S complex. The orientation and the direction of the hexasaccharide on the catK surface have changed, so that the hexasaccharide is positioned between two symmetry-related molecules. Only one M5 variant molecule of the dimer that is present in the asymmetric unit interacts with C4-S. These substitutions have changed the mode of catK binding to C4-S and, as a result, have likely affected the collagenolytic potential of the variant. The data presented here support our hypothesis that distinct catK/C4-S interactions are necessary for the collagenolytic activity of the enzyme.


    Organizational Affiliation

    Group in Protein Structure and Function, Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
A, E
215Homo sapiensMutation(s): 6 
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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Download CCD File 
A, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
E64
Query on E64

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Download CCD File 
A, E
N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
C15 H30 N5 O5
QPQNJAXBPHVASB-QWRGUYRKSA-O
 Ligand Interaction
BDP
Query on BDP

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Download CCD File 
A
BETA-D-GLUCOPYRANURONIC ACID
D-GLUCURONIC ACID
C6 H10 O7
AEMOLEFTQBMNLQ-QIUUJYRFSA-N
 Ligand Interaction
ASG
Query on ASG

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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: 2.242 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 140.564α = 90.00
b = 42.014β = 94.19
c = 87.509γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-01-15
    Type: Database references