2XXL

Crystal structure of drosophila Grass clip serine protease of Toll pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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This is version 2.0 of the entry. See complete history


Literature

Structure-Function Analysis of Grass Clip Serine Protease Involved in Drosophila Toll Pathway Activation.

Kellenberger, C.Leone, P.Coquet, L.Jouenne, T.Reichhart, J.M.Roussel, A.

(2011) J Biol Chem 286: 12300

  • DOI: 10.1074/jbc.M110.182741
  • Primary Citation of Related Structures:  
    2XXL

  • PubMed Abstract: 
  • Grass is a clip domain serine protease (SP) involved in a proteolytic cascade triggering the Toll pathway activation of Drosophila during an immune response. Epistasic studies position it downstream of the apical protease ModSP and upstream of the terminal protease Spaetzle-processing enzyme ...

    Grass is a clip domain serine protease (SP) involved in a proteolytic cascade triggering the Toll pathway activation of Drosophila during an immune response. Epistasic studies position it downstream of the apical protease ModSP and upstream of the terminal protease Spaetzle-processing enzyme. Here, we report the crystal structure of Grass zymogen. We found that Grass displays a rather deep active site cleft comparable with that of proteases of coagulation and complement cascades. A key distinctive feature is the presence of an additional loop (75-loop) in the proximity of the activation site localized on a protruding loop. All biochemical attempts to hydrolyze the activation site of Grass failed, strongly suggesting restricted access to this region. The 75-loop is thus proposed to constitute an original mechanism to prevent spontaneous activation. A comparison of Grass with clip serine proteases of known function involved in analogous proteolytic cascades allowed us to define two groups, according to the presence of the 75-loop and the conformation of the clip domain. One group (devoid of the 75-loop) contains penultimate proteases whereas the other contains terminal proteases. Using this classification, Grass appears to be a terminal protease. This result is evaluated according to the genetic data documenting Grass function.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques UMR6098, Parc Scientifique et Technologique de Luminy, 13288 Marseille Cedex 09, France. Christine.Kellenberger@afmb.univ-mrs.fr



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GRAM-POSITIVE SPECIFIC SERINE PROTEASE, ISOFORM BA, B408Drosophila melanogasterMutation(s): 0 
Gene Names: grassc-SP1CG5896
EC: 3.4.21.4 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for Q9VB68 (Drosophila melanogaster)
Explore Q9VB68 
Go to UniProtKB:  Q9VB68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VB68
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseC, D, E 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.26α = 90
b = 92.04β = 90
c = 113.34γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary