3H6S

Structure of clitocypin - cathepsin V complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Versatile loops in mycocypins inhibit three protease families.

Renko, M., Sabotic, J., Mihelic, M., Brzin, J., Kos, J., Turk, D.

(2010) J.Biol.Chem. 285: 308-316

  • DOI: 10.1074/jbc.M109.043331
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Mycocypins, clitocypins and macrocypins, are cysteine protease inhibitors isolated from the mushrooms Clitocybe nebularis and Macrolepiota procera. Lack of sequence homology to other families of protease inhibitors suggested that mycocypins inhibit t ...

    Mycocypins, clitocypins and macrocypins, are cysteine protease inhibitors isolated from the mushrooms Clitocybe nebularis and Macrolepiota procera. Lack of sequence homology to other families of protease inhibitors suggested that mycocypins inhibit their target cysteine protease by a unique mechanism and that a novel fold may be found. The crystal structures of the complex of clitocypin with the papain-like cysteine protease cathepsin V and of macrocypin and clitocypin alone have revealed yet another motif of binding to papain like-cysteine proteases, which in a yet unrevealed way occludes the catalytic residue. The binding is associated with a peptide-bond flip of glycine that occurs before or concurrently with the inhibitor docking. Mycocypins possess a beta-trefoil fold, the hallmark of Kunitz-type inhibitors. It is a tree-like structure with two loops in the root region, a stem comprising a six-stranded beta-barrel, and two layers of loops (6 + 3) in the crown region. The two loops that bind to cysteine cathepsins belong to the lower layer of the crown loops, whereas a single loop from the crown region can inhibit trypsin or asparaginyl endopeptidase, as demonstrated by site-directed mutagenesis. These loops present a versatile surface with the potential to bind to additional classes of proteases. When appropriately engineered, they could provide the basis for possible exploitation in crop protection.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular, Jozef Stefan Institute,Jamova 39, 1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin L2
A, B, C, D
221Homo sapiensMutation(s): 2 
Gene Names: CTSV (CATL2, CTSL2, CTSU)
EC: 3.4.22.43
Find proteins for O60911 (Homo sapiens)
Go to Gene View: CTSV
Go to UniProtKB:  O60911
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Clitocypin analog
E, F, G, H
152Clitocybe nebularisMutation(s): 2 
Gene Names: clt5
Find proteins for Q3Y9I6 (Clitocybe nebularis)
Go to UniProtKB:  Q3Y9I6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, C, D, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
A, B, C, D
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
SME
Query on SME
E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 97.180α = 90.00
b = 177.760β = 90.00
c = 96.180γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
AMoREphasing
DENZOdata reduction
MAINrefinement
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2016-12-21
    Type: Structure summary
  • Version 1.3: 2017-11-01
    Type: Advisory, Refinement description