1MZA

crystal structure of human pro-granzyme K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.3 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, 1MZD

  • 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 involved in apoptosis ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
pro-granzyme KA240Homo sapiensMutation(s): 1 
Gene Names: GZMKTRYP2
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P49863 (Homo sapiens)
Explore P49863 
Go to UniProtKB:  P49863
PHAROS:  P49863
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49863
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.465α = 90
b = 78.158β = 90
c = 83.629γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references