5MS4

Kallikrein-related peptidase 8 leupeptin inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 2.1 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
  • Structures With Same Primary Citation

  • 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

    Division of Structural Biology, Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria. peter.goettig@sbg.ac.at.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-8
A, B, C, D
228Homo sapiensMutation(s): 0 
Gene Names: KLK8NRPNPRSS19TADG14UNQ283/PRO322
EC: 3.4.21.118
Find proteins for O60259 (Homo sapiens)
Go to UniProtKB:  O60259
NIH Common Fund Data Resources
PHAROS  O60259
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEUPEPTIN
E, F, G, H
4synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TBU
Query on TBU

Download CCD File 
A
TERTIARY-BUTYL ALCOHOL
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000216
Query on PRD_000216
E, F, G, HLEUPEPTINOligopeptide /  Enzyme inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AR7
Query on AR7
E,F,G,H
PEPTIDE-LIKEC6 H17 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.103α = 90
b = 46.045β = 91.4
c = 103.349γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references
  • Version 2.0: 2019-09-18
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-10-09
    Changes: Data collection, Derived calculations