5MS4 | pdb_00005ms4

Kallikrein-related peptidase 8 leupeptin inhibitor complex

• PDB DOI: https://doi.org/10.2210/pdb5MS4/pdb

• Classification: Hydrolase/Inhibitor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-30 Released: 2018-01-17 
• Deposition Author(s): Debela, M., Magdolen, V., Skala, W., Bode, W., Brandstetter, H., Goettig, P.
• Funding Organization(s): Austrian Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.259 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

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

• PubMed: 30013126 
• DOI: https://doi.org/10.1038/s41598-018-29058-6
• Primary Citation Related Structures: 
  5MS4


• 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 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.

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Organizational Affiliation: 
• Max-Planck-Institut für Biochemie, Proteinase Research Group, 82152, Martinsried, Germany.
Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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.
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA.
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.
German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
Division of Structural Biology, Department of Biosciences, University of Salzburg, 5020, Salzburg, Austria. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 100.04 kDa 
• Atom Count: 8,120 
• Modeled Residue Count: 928 
• Deposited Residue Count: 928 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallikrein-8	A, B, C, D	228	Homo sapiens	Mutation(s): 0  Gene Names: KLK8, NRPN, PRSS19, TADG14, UNQ283/PRO322 EC: 3.4.21.118
UniProt & NIH Common Fund Data Resources
Find proteins for O60259 (Homo sapiens) Explore O60259  Go to UniProtKB:  O60259
PHAROS:  O60259 GTEx:  ENSG00000129455

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LEUPEPTIN	E, F, G, H	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBU	I [auth A], J [auth A], K [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N
CA	L [auth A], M [auth B], N [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AR7	E, F, G, H	PEPTIDE-LIKE	C6 H17 N4 O2		ARG

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000216	E, F, G, H	LEUPEPTIN	Oligopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.259 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.103	α = 90
b = 46.045	β = 91.4
c = 103.349	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Debela, M., Magdolen, V., Skala, W., Bode, W., Brandstetter, H., Goettig, P.

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Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P25003-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
• Version 2.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary