PDBsum entry 3h6s

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protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
Protein chains
220 a.a. *
152 a.a. *
SO4 ×6
Waters ×857
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Strucure of clitocypin - cathepsin v complex
Structure: Cathepsin l2. Chain: a, b, c, d. Synonym: cathepsin v, cathepsin u. Engineered: yes. Clitocypin analog. Chain: e, f, g, h. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ctsl2, catl2, ctsu, ctsv, unq268/pro305. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Clitocybe nebularis. Clouded agaric. Organism_taxid: 117024.
2.22Å     R-factor:   0.182     R-free:   0.239
Authors: M.Renko,J.Sabotic,J.Brzin,D.Turk
Key ref:
M.Renko et al. (2009). Versatile loops in mycocypins inhibit three protease families. J Biol Chem, 285, 308-316. PubMed id: 19846555 DOI: 10.1074/jbc.M109.043331
23-Apr-09     Release date:   20-Oct-09    
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Protein chains
Pfam   ArchSchema ?
O60911  (CATL2_HUMAN) -  Cathepsin L2
334 a.a.
220 a.a.*
Protein chains
Pfam   ArchSchema ?
Q3Y9I6  (CLIT5_CLINE) -  Clitocypin-5
152 a.a.
152 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.  - Cathepsin V.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The recombinant enzyme hydrolyzes proteins (serum albumin, collagen) and synthetic substrates (Z-Phe-Arg-NHMec > Z-Leu-Arg-NHMec > Z-Val-Arg-NHMec).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   3 terms 
  Biochemical function     peptidase inhibitor activity     3 terms  


DOI no: 10.1074/jbc.M109.043331 J Biol Chem 285:308-316 (2009)
PubMed id: 19846555  
Versatile loops in mycocypins inhibit three protease families.
M.Renko, J.Sabotic, M.Mihelic, J.Brzin, J.Kos, D.Turk.
Mycocypins, clitocypin 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 prior to 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 2 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, while 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.
  Selected figure(s)  
Figure 2.
Orientation of the Gly-24-Gly-25 peptide bond in the two clitocypin molecules. The 2F[obs] − F[calc] electron density map is contoured at 1 σ. The bonds of glycine 24 are shown in green, whereas the rest of the chain is shown in red for oxygen, blue for nitrogen, and orange for carbon. The Gly-24–Gly-25 peptide bond is flexible and can exist in either orientation.
Figure 3.
The cathepsin V-clitocypin complex. A, shown is the view along the active site cleft. B, shown is the view perpendicular to the active site cleft. The folds of cathepsin V and clitocypin are shown in gray and red. The catalytic cysteine is shown in yellow. Clitocypin binds into the active site of cathepsin V in the orientation of a fallen tree with the trunk and roots pointing sideways and up. The wedge shaped structure fills the active site cleft along its whole length.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 285, 308-316) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20860624 M.Renko, U.Požgan, D.Majera, and D.Turk (2010).
Stefin A displaces the occluding loop of cathepsin B only by as much as required to bind to the active site cleft.
  FEBS J, 277, 4338-4345.
PDB code: 3k9m
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