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PDBsum entry 1spj

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protein ligands metals links
Hydrolase PDB id
1spj
Jmol
Contents
Protein chain
236 a.a. *
Ligands
NAG
ACY
Metals
_CA ×2
Waters ×354
* Residue conservation analysis
PDB id:
1spj
Name: Hydrolase
Title: Structure of mature human tissue kallikrein (human kallikrei klk1) at 1.70 angstrom resolution with vacant active site
Structure: Kallikrein 1. Chain: a. Synonym: tissue kallikrein, kidney/pancreas/salivary gland kallikrein. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: klk1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Resolution:
1.70Å     R-factor:   0.172     R-free:   0.202
Authors: G.Laxmikanthan,S.I.Blaber,M.J.Bernett,M.Blaber
Key ref:
G.Laxmikanthan et al. (2005). 1.70 A X-ray structure of human apo kallikrein 1: structural changes upon peptide inhibitor/substrate binding. Proteins, 58, 802-814. PubMed id: 15651049 DOI: 10.1002/prot.20368
Date:
16-Mar-04     Release date:   25-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06870  (KLK1_HUMAN) -  Kallikrein-1
Seq:
Struc:
262 a.a.
236 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.35  - Tissue kallikrein.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage of Arg-|-Xaa bonds in small molecule substrates. Highly selective action to release kallidin (lysyl-bradykinin) from kininogen involves hydrolysis of Met-|-Xaa or Leu-|-Xaa. The rat enzyme is unusual in liberating bradykinin directly from autologous kininogens by cleavage at two Arg-|-Xaa bonds.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular vesicular exosome   2 terms 
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1002/prot.20368 Proteins 58:802-814 (2005)
PubMed id: 15651049  
 
 
1.70 A X-ray structure of human apo kallikrein 1: structural changes upon peptide inhibitor/substrate binding.
G.Laxmikanthan, S.I.Blaber, M.J.Bernett, I.A.Scarisbrick, M.A.Juliano, M.Blaber.
 
  ABSTRACT  
 
Human kallikreins are serine proteases that comprise a recently identified large and closely related 15-member family. The kallikreins include both regulatory- and degradative-type proteases, impacting a variety of physiological processes including regulation of blood pressure, neuronal health, and the inflammatory response. While the function of the majority of the kallikreins remains to be elucidated, two members are useful biomarkers for prostate cancer and several others are potentially useful biomarkers for breast cancer, Alzheimer's, and Parkinson's disease. Human tissue kallikrein (human K1) is the best functionally characterized member of this family, and is known to play an important role in blood pressure regulation. As part of this function, human K1 exhibits unique dual-substrate specificity in hydrolyzing low molecular weight kininogen between both Arg-Ser and Met-Lys sequences. We report the X-ray crystal structure of mature, active recombinant human apo K1 at 1.70 A resolution. The active site exhibits structural features intermediate between that of apo and pro forms of known kallikrein structures. The S2 to S2' pockets demonstrate a variety of conformational changes in comparison to the porcine homolog of K1 in complex with peptide inhibitors, including the displacement of an extensive solvent network. These results indicate that the binding of a peptide substrate contributes to a structural rearrangement of the active-site Ser 195 resulting in a catalytically competent juxtaposition with the active-site His 57. The solvent networks within the S1 and S1' pockets suggest how the Arg-Ser and Met-Lys dual substrate specificity of human K1 is accommodated.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Relaxed stereo diagram ribbon drawing of the human apo K1 structure (light grey) and the overlaid kallikrein loop regions of horse K3 (1GVZ, magenta), porcine K1 (2PKA, red), mouse GK3 (1SGF, blue), mouse GK13 (1AO5, green) and rat GK2 (1TON, yellow), with the human K1 kallikrein loop indicated in dark grey. The active site His 57, Asp 102, and Ser 195 residues in human K1, as well as the Asp 189 at the base of the S1 pocket are indicated in wire frame representation. The location of the S1 and S1 pockets are indicated. The carbohydrate moiety attached to Asn 95, observed in the human K1, mouse GK3 and mouse GK13 structures, is also indicated in wire frame shown.
Figure 3.
Figure 3. Top: relaxed stereo diagram of the active site of human apo K1, with the active site Ser 195 gauche+ rotamer shown, overlaid with the active site in mouse apo K8 (1NPM; grey). Bottom: relaxed stereo diagram of the active site of human apo K1, with the active site Ser 195 gauche- rotamer shown, overlaid with the active site of pro human K6 (1GVL; grey).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 802-814) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21072173 A.Pavlopoulou, G.Pampalakis, I.Michalopoulos, and G.Sotiropoulou (2010).
Evolutionary history of tissue kallikreins.
  PLoS One, 5, e13781.  
20615447 P.Goettig, V.Magdolen, and H.Brandstetter (2010).
Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).
  Biochimie, 92, 1546-1567.  
19819870 G.Sotiropoulou, G.Pampalakis, and E.P.Diamandis (2009).
Functional roles of human kallikrein-related peptidases.
  J Biol Chem, 284, 32989-32994.  
18778305 A.G.Vandell, N.Larson, G.Laxmikanthan, M.Panos, S.I.Blaber, M.Blaber, and I.A.Scarisbrick (2008).
Protease-activated receptor dependent and independent signaling by kallikreins 1 and 6 in CNS neuron and astroglial cell lines.
  J Neurochem, 107, 855-870.  
18844446 A.R.Lima, F.M.Alves, P.F.Angelo, D.Andrade, S.I.Blaber, M.Blaber, L.Juliano, and M.A.Juliano (2008).
S(1)' and S(2)' subsite specificities of human plasma kallikrein and tissue kallikrein 1 for the hydrolysis of peptides derived from the bradykinin domain of human kininogen.
  Biol Chem, 389, 1487-1494.  
18500692 H.Koistinen, G.Wohlfahrt, J.M.Mattsson, P.Wu, J.Lahdenperä, and U.H.Stenman (2008).
Novel small molecule inhibitors for prostate-specific antigen.
  Prostate, 68, 1143-1151.  
18359858 H.X.Li, B.Y.Hwang, G.Laxmikanthan, S.I.Blaber, M.Blaber, P.A.Golubkov, P.Ren, B.L.Iverson, and G.Georgiou (2008).
Substrate specificity of human kallikreins 1 and 6 determined by phage display.
  Protein Sci, 17, 664-672.  
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.  
17158887 C.A.Borgoño, I.P.Michael, N.Komatsu, A.Jayakumar, R.Kapadia, G.L.Clayman, G.Sotiropoulou, and E.P.Diamandis (2007).
A potential role for multiple tissue kallikrein serine proteases in epidermal desquamation.
  J Biol Chem, 282, 3640-3652.  
17823117 H.Yoon, G.Laxmikanthan, J.Lee, S.I.Blaber, A.Rodriguez, J.M.Kogot, I.A.Scarisbrick, and M.Blaber (2007).
Activation profiles and regulatory cascades of the human kallikrein-related peptidases.
  J Biol Chem, 282, 31852-31864.  
17890078 I.Botos, and A.Wlodawer (2007).
The expanding diversity of serine hydrolases.
  Curr Opin Struct Biol, 17, 683-690.  
17909180 M.Debela, P.Hess, V.Magdolen, N.M.Schechter, T.Steiner, R.Huber, W.Bode, and P.Goettig (2007).
Chymotryptic specificity determinants in the 1.0 A structure of the zinc-inhibited human tissue kallikrein 7.
  Proc Natl Acad Sci U S A, 104, 16086-16091.
PDB codes: 2qxg 2qxh 2qxi 2qxj
16800726 C.D.Petraki, P.A.Papanastasiou, V.N.Karavana, and E.P.Diamandis (2006).
Cellular distribution of human tissue kallikreins: immunohistochemical localization.
  Biol Chem, 387, 653-663.  
16740631 M.Debela, V.Magdolen, N.Schechter, M.Valachova, F.Lottspeich, C.S.Craik, Y.Choe, W.Bode, and P.Goettig (2006).
Specificity profiling of seven human tissue kallikreins reveals individual subsite preferences.
  J Biol Chem, 281, 25678-25688.  
16800729 N.Heuzé-Vourc'h, M.Aïnciburu, C.Planque, M.Brillard-Bourdet, C.Ott, C.Jolivet-Reynaud, and Y.Courty (2006).
Recombinant kallikrein expression: site-specific integration for hK6 production in human cells.
  Biol Chem, 387, 687-695.  
16321973 P.F.Angelo, A.R.Lima, F.M.Alves, S.I.Blaber, I.A.Scarisbrick, M.Blaber, L.Juliano, and M.A.Juliano (2006).
Substrate specificity of human kallikrein 6: salt and glycosaminoglycan activation effects.
  J Biol Chem, 281, 3116-3126.  
16800733 T.Kishi, S.M.Cloutier, C.Kündig, D.Deperthes, and E.P.Diamandis (2006).
Activation and enzymatic characterization of recombinant human kallikrein 8.
  Biol Chem, 387, 723-731.  
16199530 J.Tang, C.L.Yu, S.R.Williams, E.Springman, D.Jeffery, P.A.Sprengeler, A.Estevez, J.Sampang, W.Shrader, J.Spencer, W.Young, M.McGrath, and B.A.Katz (2005).
Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein.
  J Biol Chem, 280, 41077-41089.
PDB codes: 2anw 2any
16170411 N.L.Clark, and W.J.Swanson (2005).
Pervasive adaptive evolution in primate seminal proteins.
  PLoS Genet, 1, e35.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.