Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.55 kDa 
• Atom Count: 6434 
• Modelled Residue Count: 708 
• Deposited Residue Count: 816 
• Unique protein chains: 1

2XXL

Crystal structure of drosophila Grass clip serine protease of Toll pathway

• PDB DOI: 10.2210/pdb2XXL/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2010-11-10 Released: 2011-02-09 
• Deposition Author(s): Kellenberger, C., Leone, P., Coquet, L., Jouenne, T., Reichhart, J.M., Roussel, A.

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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 

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

• PubMed: 21310954 
• 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. 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.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques UMR6098, Parc Scientifique et Technologique de Luminy, 13288 Marseille Cedex 09, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GRAM-POSITIVE SPECIFIC SERINE PROTEASE, ISOFORM B	A, B	408	Drosophila melanogaster	Mutation(s): 0  Gene Names: grass, c-SP1, CG5896 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	C, D, E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	G [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 78.26	α = 90
b = 92.04	β = 90
c = 113.34	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-10 
• Released Date: 2011-02-09 
Deposition Author(s): Kellenberger, C., Leone, P., Coquet, L., Jouenne, T., Reichhart, J.M., Roussel, A.

Revision History  

• 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