5Z5O

Structure of Pycnonodysostosis disease related I249T mutant of human cathepsin K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Not all pycnodysostosis-related mutants of human cathepsin K are inactive - crystal structure and biochemical studies of an active mutant I249T.

Roy, S.Das Chakraborty, S.Biswas, S.

(2018) FEBS J 285: 4265-4280

  • DOI: 10.1111/febs.14655
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human cathepsin K (CTSK) is a collagenolytic lysosomal cysteine protease that plays an important role in bone turnover. Mutation in CTSK gene is associated with loss of collagenolytic activity of CTSK leading to an autosomal recessive bone disorder c ...

    Human cathepsin K (CTSK) is a collagenolytic lysosomal cysteine protease that plays an important role in bone turnover. Mutation in CTSK gene is associated with loss of collagenolytic activity of CTSK leading to an autosomal recessive bone disorder called pycnodysostosis. Although a number of pycnodysostotic missense mutations have been reported, underlying mechanism of the disease is not clear. In this study, we investigated in vitro six recombinant pycnodysostosis-related mutants of human CTSK (G79E, I249T, G243E, G303E, G319C and Q187P). While all the mutants, like wild-type, show similar high levels of expression in Escherichia coli, four of them (G79E, G303E, G319C and Q187P) are inactive, unstable and spontaneously degrade during purification process. In contrast, proteolytic/collagenolytic activity, zymogen activation kinetics and stability of G243E and I249T mutants are nominally affected. Crystal structure of I249T at 1.92 Å resolution shows that the mutation in R-domain causes conformational changes of a surface loop in the L-domain although the catalytic cleft remains unaltered. Molecular simulation, normal mode analysis and fluorescence lifetime measurement eliminated the possibility that the change in L-domain surface loop orientation is a crystallization artefact. CD-based thermal melting profile indicates that stability of I249T is significantly higher than wild-type. Our studies first time reports that pycnodysostosis-related mutations do not always lead to complete loss of general proteolytic activity or specific collagenolytic activity of CTSK. The first crystal structure of a pycnodysostotic mutant (I249T) provides critical information that may pave new avenues towards understanding the disease at molecular level. DATABASE: The atomic co-ordinates and structure factors for I249T mutant of human CTSK (codes 5Z5O) have been deposited in the Protein Data Bank (http://wwpdb.org/).


    Organizational Affiliation

    Homi Bhaba National Institute, Mumbai, India.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
A
335Homo sapiensMutation(s): 2 
Gene Names: CTSKCTSOCTSO2
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Go to UniProtKB:  P43235
NIH Common Fund Data Resources
PHAROS  P43235

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cathepsin K
B
94Homo sapiensMutation(s): 0 
Gene Names: CTSKCTSOCTSO2
EC: 3.4.22.38
Find proteins for P43235 (Homo sapiens)
Go to UniProtKB:  P43235
NIH Common Fund Data Resources
PHAROS  P43235
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEB
Query on SEB
A
L-PEPTIDE LINKINGC10 H13 N O5 SSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.1α = 90
b = 67.27β = 91.83
c = 82.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
pointlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-19 
  • Released Date: 2018-09-26 
  • Deposition Author(s): Biswas, S., Roy, S.

Funding OrganizationLocationGrant Number
DSTIndia--

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references