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:  
    3H6Q, 3H6R, 3H6S

  • 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 their ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cathepsin L2 A, B, C, D221Homo sapiensMutation(s): 2 
Gene Names: CTSL2, CATL2, CTSU, CTSV, UNQ268/PRO305
EC: 3.4.22.43
Find proteins for O60911 (Homo sapiens)
Explore O60911 
Go to UniProtKB:  O60911
NIH Common Fund Data Resources
PHAROS:  O60911
GTEx:  ENSG00000136943
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Clitocypin analog E, F, G, H152Clitocybe nebularisMutation(s): 2 
Gene Names: clt5
Find proteins for Q3Y9I6 (Clitocybe nebularis)
Explore Q3Y9I6 
Go to UniProtKB:  Q3Y9I6
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH		A,B,C,DL-PEPTIDE LINKINGC4 H9 N O2 S2CYS
SME
Query on SME		E,F,G,HL-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 = 97.18α = 90
b = 177.76β = 90
c = 96.18γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
AMoREphasing
MAINrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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