1MZD

crystal structure of human pro-granzyme K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.2-A Crystal Structure of Human Pro-granzyme K Reveals a Rigid Zymogen with Unusual Features

Hink-Schauer, C.Estebanez-Perpina, E.Wilharm, E.Fuentes-Prior, P.Klinkert, W.Bode, W.Jenne, D.E.

(2002) J.BIOL.CHEM. 277: 50923-50933

  • DOI: 10.1074/jbc.M207962200
  • Primary Citation of Related Structures:  1MZA

  • PubMed Abstract: 
  • Granzyme K (GzmK) belongs to a family of trypsin-like serine proteases localized in electron dense cytoplasmic granules of activated natural killer and cytotoxic T-cells. Like the related granzymes A and B, GzmK can trigger DNA fragmentation and is i ...

    Granzyme K (GzmK) belongs to a family of trypsin-like serine proteases localized in electron dense cytoplasmic granules of activated natural killer and cytotoxic T-cells. Like the related granzymes A and B, GzmK can trigger DNA fragmentation and is involved in apoptosis. We expressed the Ser(195) --> Ala variant of human pro-GzmK in Escherichia coli, crystallized it, and determined its 2.2-A x-ray crystal structure. Pro-GzmK possesses a surprisingly rigid structure, which is most similar to activated serine proteases, in particular complement factor D, and not their proforms. The N-terminal peptide Met(14)-Ile(17) projects freely into solution and can be readily approached by cathepsin C, the natural convertase of pro-granzymes. The pre-shaped S1 pocket is occupied by the ion paired residues Lys(188B)-Asp(194) and is hence not available for proper substrate binding. The Ser(214)-Cys(220) segment, which normally provides a template for substrate binding, bulges out of the active site and is distorted. With analogy to complement factor D, we suggest that this strand will maintain its non-productive conformation in mature GzmK, mainly due to the unusual residues Gly(215), Glu(219), and Val(94). We hypothesize that GzmK is proteolytically active only toward specific, as yet unidentified substrates, which upon approach transiently induce a functional active-site conformation.


    Organizational Affiliation

    Department of Neuroimmunology, Max-Planck-Institute of Neurobiology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18a, Planegg-Martinsried D-82152, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
pro-granzyme K
A
240Homo sapiensGene Names: GZMK (TRYP2)
EC: 3.4.21.-
Find proteins for P49863 (Homo sapiens)
Go to Gene View: GZMK
Go to UniProtKB:  P49863
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.750α = 90.00
b = 78.860β = 90.00
c = 85.250γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
CCP4data scaling
CCP4data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance