5MS4

Kallikrein-related peptidase 8 leupeptin inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin.

Debela, M.Magdolen, V.Skala, W.Elsasser, B.Schneider, E.L.Craik, C.S.Biniossek, M.L.Schilling, O.Bode, W.Brandstetter, H.Goettig, P.

(2018) Sci Rep 8: 10705-10705

  • DOI: 10.1038/s41598-018-29058-6

  • PubMed Abstract: 
  • Human KLK8/neuropsin, a kallikrein-related serine peptidase, is mostly expressed in skin and the hippocampus regions of the brain, where it regulates memory formation by synaptic remodeling. Substrate profiles of recombinant KLK8 were analyzed with p ...

    Human KLK8/neuropsin, a kallikrein-related serine peptidase, is mostly expressed in skin and the hippocampus regions of the brain, where it regulates memory formation by synaptic remodeling. Substrate profiles of recombinant KLK8 were analyzed with positional scanning using fluorogenic tetrapeptides and the proteomic PICS approach, which revealed the prime side specificity. Enzyme kinetics with optimized substrates showed stimulation by Ca 2+ and inhibition by Zn 2+ , which are physiological regulators. Crystal structures of KLK8 with a ligand-free active site and with the inhibitor leupeptin explain the subsite specificity and display Ca 2+ bound to the 75-loop. The variants D70K and H99A confirmed the antagonistic role of the cation binding sites. Molecular docking and dynamics calculations provided insights in substrate binding and the dual regulation of activity by Ca 2+ and Zn 2+ , which are important in neuron and skin physiology. Both cations participate in the allosteric surface loop network present in related serine proteases. A comparison of the positional scanning data with substrates from brain suggests an adaptive recognition by KLK8, based on the tertiary structures of its targets. These combined findings provide a comprehensive picture of the molecular mechanisms underlying the enzyme activity of KLK8.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Proteinase Research Group, 82152, Martinsried, Germany.,Division of Structural Biology, Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, 81675, München, Germany.,Division of Structural Biology, Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria. peter.goettig@sbg.ac.at.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.,Institute of Molecular Medicine and Cell Research, University of Freiburg, 79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-8
A, B, C, D
228Homo sapiensMutation(s): 0 
Gene Names: KLK8 (NRPN, PRSS19, TADG14)
EC: 3.4.21.118
Find proteins for O60259 (Homo sapiens)
Go to Gene View: KLK8
Go to UniProtKB:  O60259
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SVC
Query on SVC

Download SDF File 
Download CCD File 
A, B, C, D
N-acetyl-L-leucyl-N-[(2S)-5-carbamimidamido-1-hydroxypentan-2-yl]-L-leucinamide
LEUPEPTIN
C20 H40 N6 O4
VGABNAQMXSGCOP-ULQDDVLXSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TBU
Query on TBU

Download SDF File 
Download CCD File 
A
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.103α = 90.00
b = 46.045β = 91.40
c = 103.349γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP25003-B21

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references