2ZKS

Structural insights into the proteolytic machinery of apoptosis-inducing Granzyme M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for proteolytic specificity of the human apoptosis-inducing granzyme M

Wu, L.Wang, L.Hua, G.Liu, K.Yang, X.Zhai, Y.Bartlam, M.Sun, F.Fan, Z.

(2009) J.Immunol. 183: 421-429

  • DOI: 10.4049/jimmunol.0803088
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Granzyme M (GzmM), a unique serine protease constitutively expressed in NK cells, is important for granule-mediated cytolysis and can induce rapid caspase-dependent apoptosis of tumor cells. However, few substrates of GzmM have been reported to date, ...

    Granzyme M (GzmM), a unique serine protease constitutively expressed in NK cells, is important for granule-mediated cytolysis and can induce rapid caspase-dependent apoptosis of tumor cells. However, few substrates of GzmM have been reported to date, and the mechanism by which this enzyme recognizes and hydrolyzes substrates is unknown. To provide structural insights into the proteolytic specificity of human GzmM (hGzmM), crystal structures of wild-type hGzmM, the inactive D86N-GzmM mutant with bound peptide substrate, and the complexes with a catalytic product and with a tetrapeptide chloromethylketone inhibitor were solved to 1.96 A, 2.30 A, 2.17 A and 2.70 A, respectively. Structure-based mutagenesis revealed that the N terminus and catalytic triad of hGzmM are most essential for proteolytic function. In particular, D86N-GzmM was found to be an ideal inactive enzyme for functional studies. Structural comparisons indicated a large conformational change of the L3 loop upon substrate binding, and suggest this loop mediates the substrate specificity of hGzmM. Based on the complex structure of GzmM with its catalytic product, a tetrapeptide chloromethylketone inhibitor was designed and found to specifically block the catalytic activity of hGzmM.


    Organizational Affiliation

    Center for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Granzyme M
A
240Homo sapiensMutation(s): 0 
Gene Names: GZMM (MET1)
EC: 3.4.21.-
Find proteins for P51124 (Homo sapiens)
Go to Gene View: GZMM
Go to UniProtKB:  P51124
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
hGzmM inhibitor
C
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
0QE
Query on 0QE
C
NON-POLYMERC H3 Cl

--

ACE
Query on ACE
C
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.223 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.671α = 90.00
b = 74.671β = 90.00
c = 113.557γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MAR345dtbdata collection
REFMACrefinement
MOSFLMdata reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description