5LPE

Kallikrein-related peptidase 10 complex with Zn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the Zn2+ inhibition of the zymogen-like kallikrein-related peptidase 10.

Debela, M.Magdolen, V.Bode, W.Brandstetter, H.Goettig, P.

(2016) Biol.Chem. 397: 1251-1264

  • DOI: 10.1515/hsz-2016-0205
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although kallikrein-related peptidase 10 (KLK10) is expressed in a variety of human tissues and body fluids, knowledge of its physiological functions is fragmentary. Similarly, the pathophysiology of KLK10 in cancer is not well understood. In some ca ...

    Although kallikrein-related peptidase 10 (KLK10) is expressed in a variety of human tissues and body fluids, knowledge of its physiological functions is fragmentary. Similarly, the pathophysiology of KLK10 in cancer is not well understood. In some cancer types, a role as tumor suppressor has been suggested, while in others elevated expression is associated with poor patient prognosis. Active human KLK10 exhibits a unique, three residue longer N-terminus with respect to other serine proteases and an extended 99-loop nearly as long as in tissue kallikrein KLK1. Crystal structures of recombinant ligand-free KLK10 and a Zn2+ bound form explain to some extent the mixed trypsin- and chymotrypsin-like substrate specificity. Zn2+-inhibition of KLK10 appears to be based on a unique mechanism, which involves direct binding and blocking of the catalytic triad. Since the disordered N-terminus and several loops adopt a zymogen-like conformation, the active protease conformation is very likely induced by interaction with the substrate, in particular at the S1 subsite and at the unusual Ser193 as part of the oxyanion hole. The KLK10 structures indicate that the N-terminus, the nearby 75-, 148-, and the 99-loops are connected in an allosteric network, which is present in other trypsin-like serine proteases with several variations.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kallikrein-10
A, B
234Homo sapiensMutation(s): 0 
Gene Names: KLK10 (NES1, PRSSL1)
EC: 3.4.21.-
Find proteins for O43240 (Homo sapiens)
Go to Gene View: KLK10
Go to UniProtKB:  O43240
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.914α = 90.00
b = 67.037β = 104.37
c = 57.768γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
AUTOMARdata collection

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: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence
  • Version 1.3: 2019-02-20
    Type: Advisory, Data collection, Derived calculations