2BDI

Human Kallikrein 4 complex with cobalt and p-aminobenzamidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.

Debela, M.Magdolen, V.Grimminger, V.Sommerhoff, C.Messerschmidt, A.Huber, R.Friedrich, R.Bode, W.Goettig, P.

(2006) J.Mol.Biol. 362: 1094-1107

  • DOI: 10.1016/j.jmb.2006.08.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers ...

    Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70-80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC50) of 16 microM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Proteinase Research Group, Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-4
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
223Homo sapiensMutation(s): 0 
Gene Names: KLK4 (EMSP1, PRSS17, PSTS)
EC: 3.4.21.-
Find proteins for Q9Y5K2 (Homo sapiens)
Go to Gene View: KLK4
Go to UniProtKB:  Q9Y5K2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBZ
Query on PBZ

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
P-AMINO BENZAMIDINE
C7 H10 N3
WPANETAWYGDRLL-UHFFFAOYSA-O
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, E, I, M
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.258 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 147.050α = 90.00
b = 73.860β = 102.41
c = 154.380γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance