PDBsum entry 2psx

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Hydrolase/hydrolase inhibitor PDB id
Protein chain
227 a.a. *
Waters ×107
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of human kallikrein 5 in complex with leup
Structure: Kallikrein-5. Chain: a. Fragment: catalytic domain. Synonym: stratum corneum tryptic enzyme, kallikrein-like pr klk-l2. Engineered: yes. Leupeptin. Chain: b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: klk5. Synthetic: yes. Other_details: chemically synthesized.
2.30Å     R-factor:   0.221     R-free:   0.269
Authors: M.Debela,W.Bode,P.Goettig
Key ref:
M.Debela et al. (2007). Structural basis of the zinc inhibition of human tissue kallikrein 5. J Mol Biol, 373, 1017-1031. PubMed id: 17881000 DOI: 10.1016/j.jmb.2007.08.042
07-May-07     Release date:   11-Sep-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9Y337  (KLK5_HUMAN) -  Kallikrein-5
293 a.a.
227 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     2 terms  


DOI no: 10.1016/j.jmb.2007.08.042 J Mol Biol 373:1017-1031 (2007)
PubMed id: 17881000  
Structural basis of the zinc inhibition of human tissue kallikrein 5.
M.Debela, P.Goettig, V.Magdolen, R.Huber, N.M.Schechter, W.Bode.
Human kallikrein 5 (hK5) is a member of the tissue kallikrein family of serine peptidases. It has trypsin-like substrate specificity, is inhibited by metal ions, and is abundantly expressed in human skin, where it is believed to play a central role in desquamation. To further understand the interaction of hK5 with substrates and metal ions, active recombinant hK5 was crystallized in complex with the tripeptidyl aldehyde inhibitor leupeptin, and structures at 2.3 A resolution were obtained with and without Zn2+. While the overall structure and the specificity of S1 pocket for basic side-chains were similar to that of hK4, a closely related family member, both differed in their interaction with Zn2+. Unlike hK4, the 75-loop of hK5 is not structured to bind a Zn2+. Instead, Zn2+ binds adjacent to the active site, becoming coordinated by the imidazole rings of His99 and His96 not present in hK4. This zinc binding is accompanied by a large shift in the backbone conformation of the 99-loop and by large movements of both His side-chains. Modeling studies show that in the absence of bound leupeptin, Zn2+ is likely further coordinated by the imidazolyl side-chain of the catalytic His57 which can, similar to equivalent His57 imidazole groups in the related rat kallikrein proteinase tonin and in an engineered metal-binding rat trypsin, rotate out of its triad position to provide the third co-ordination site of the bound Zn2+, rendering Zn2+-bound hK5 inactive. In solution, this mode of binding likely occurs in the presence of free and substrate saturated hK5, as kinetic analyses of Zn2+ inhibition indicate a non-competitive mechanism. Supporting the His57 re-orientation, Zn2+ does not fully inhibit hK5 hydrolysis of tripeptidyl substrates containing a P2-His residue. The P2 and His57 imidazole groups would lie next to each other in the enzyme-substrate complex, indicating that incomplete inhibition is due to competition between both imidazole groups for Zn2+. The His96-99-57 triad is thus suggested to be responsible for the Zn2+-mediated inhibition of hK5 catalysis.
  Selected figure(s)  
Figure 4.
Figure 4. Interactions between the inhibitor leupeptin and hK5. Standard stereo view towards the active-site region of hK5-Zn-free. (a) Stick model of leupeptin (pink, carbon; blue, nitrogen; and red oxygen atoms) and ribbon model of surrounding hK5 segments (grey color), with the Ser195-His57-Asp102 triad and the Zn^2+ ligating residues His96 and His99 (green, carbon; blue, nitrogen; and red carbon atoms) shown with full side-chains. The intra-triad and the intermolecular hydrogen bonds are given as broken lines. The carbonyl group of the P1-Arg3i group is pointing into the oxyanion hole (oah) made by Gly193 N-H and Ser195 N-H. (b) Leupeptin (stick model) shown in front of the solid Connolly surface of hK5-Zn, colored according to its negative (red, − 15 e(kT)^− ^1) and positive (blue, + 15 e(kT)^− ^1) electrostatic surface potential.
Figure 5.
Figure 5. Conformational changes induced in hK5 upon Zn^2+ binding. Standard stereo view towards the site of the inhibiting Zn^2+ ion. (a) Stick model of the 99-loop of hK5-Zn (golden, carbon; blue, nitrogen; and red, oxygen atoms) and the principal Zn^2+ (magenta sphere). The loop residues are superimposed with the final 2F[obs]–F[calc] electron density (blue network; contouring at 1σ) and the F^+[obs]–F^−[obs] anomalous difference electron density (magenta network; contouring at 10 σ) localized around the bound Zn^2+. The two Zn^2+-ligating water molecules are given as small blue spheres. The electrostatic interactions between this principal Zn^2+ and the atoms of the first coordination sphere are indicated by dotted lines. (b) Section of hK5-Zn around the 99-loop and leupeptin (stick model, with pink, carbon; blue, nitrogen; and red, oxygen atoms). The hK5 main-chain in the absence and the presence of Zn^2+ is shown as grey and golden ribbons, respectively, with residues His96, His99 and His57 given with their full side-chains (with green and orange carbons, respectively); the principal Zn^2+ is represented by a magenta sphere. (c) Section of hK5-Zn around the 99-loop and leupeptin, with the P2-Leu side-chain replaced by a His side-chain (thick stick model, with green, carbon; blue, nitrogen; and red, oxygen atoms). In addition, the side-chain of His57 (thick, orange carbon atoms) has been rotated, as in tonin, into a position (His57*, thin stick model; orange, carbon atoms; superimposed by a van der Waals surface), where it could additionally ligate the principal Zn^2+. Furthermore, the P2-His imidazolyl group has been rotated (thin stick models, with green carbon atoms) towards the Zn^2+ (P2-His*, thin stick model; green. carbon atoms; superimposed with a van der Waals surface) to show that it can replace the His57* imidazole in ligating this Zn^2+, as well as towards the active site, to show how it could replace the catalytic His57 imidazole group in the catalytic triad.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 1017-1031) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21424930 A.Ishida-Yamamoto, and M.Kishibe (2011).
Involvement of corneodesmosome degradation and lamellar granule transportation in the desquamation process.
  Med Mol Morphol, 44, 1-6.  
21072173 A.Pavlopoulou, G.Pampalakis, I.Michalopoulos, and G.Sotiropoulou (2010).
Evolutionary history of tissue kallikreins.
  PLoS One, 5, e13781.  
20180638 J.E.Swedberg, Veer, and J.M.Harris (2010).
Natural and engineered kallikrein inhibitors: an emerging pharmacopoeia.
  Biol Chem, 391, 357-374.  
20302517 N.Beaufort, K.Plaza, D.Utzschneider, A.Schwarz, J.M.Burkhart, S.Creutzburg, M.Debela, M.Schmitt, C.Ries, and V.Magdolen (2010).
Interdependence of kallikrein-related peptidases in proteolytic networks.
  Biol Chem, 391, 581-587.  
20337595 N.Beaufort, P.Seweryn, Bentzmann, A.Tang, J.Kellermann, N.Grebenchtchikov, M.Schmitt, C.P.Sommerhoff, D.Pidard, and V.Magdolen (2010).
Activation of human pro-urokinase by unrelated proteases secreted by Pseudomonas aeruginosa.
  Biochem J, 428, 473-482.  
20615447 P.Goettig, V.Magdolen, and H.Brandstetter (2010).
Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).
  Biochimie, 92, 1546-1567.  
20544292 Y.Inoue, T.Yokobori, T.Yokoe, Y.Toiyama, C.Miki, K.Mimori, M.Mori, and M.Kusunoki (2010).
Clinical significance of human kallikrein7 gene expression in colorectal cancer.
  Ann Surg Oncol, 17, 3037-3042.  
18627286 A.J.Ramsay, J.C.Reid, M.N.Adams, H.Samaratunga, Y.Dong, J.A.Clements, and J.D.Hooper (2008).
Prostatic trypsin-like kallikrein-related peptidases (KLKs) and other prostate-expressed tryptic proteinases as regulators of signalling via proteinase-activated receptors (PARs).
  Biol Chem, 389, 653-668.  
18844454 J.A.Clements (2008).
Reflections on the tissue kallikrein and kallikrein-related peptidase family - from mice to men - what have we learnt in the last two decades?
  Biol Chem, 389, 1447-1454.  
18627343 M.Debela, N.Beaufort, V.Magdolen, N.M.Schechter, C.S.Craik, M.Schmitt, W.Bode, and P.Goettig (2008).
Structures and specificity of the human kallikrein-related peptidases KLK 4, 5, 6, and 7.
  Biol Chem, 389, 623-632.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.