2B9L

Crystal structure of prophenoloxidase activating factor-II from the beetle Holotrichia diomphalia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a clip-domain serine protease and functional roles of the clip domains.

Piao, S.Song, Y.L.Kim, J.H.Park, S.Y.Park, J.W.Lee, B.L.Oh, B.H.Ha, N.C.

(2005) Embo J. 24: 4404-4414

  • DOI: 10.1038/sj.emboj.7600891

  • PubMed Abstract: 
  • Clip-domain serine proteases (SPs) are the essential components of extracellular signaling cascades in various biological processes, especially in embryonic development and the innate immune responses of invertebrates. They consist of a chymotrypsin- ...

    Clip-domain serine proteases (SPs) are the essential components of extracellular signaling cascades in various biological processes, especially in embryonic development and the innate immune responses of invertebrates. They consist of a chymotrypsin-like SP domain and one or two clip domains at the N-terminus. Prophenoloxidase-activating factor (PPAF)-II, which belongs to the noncatalytic clip-domain SP family, is indispensable for the generation of the active phenoloxidase leading to melanization, a major defense mechanism of insects. Here, the crystal structure of PPAF-II reveals that the clip domain adopts a novel fold containing a central cleft, which is distinct from the structures of defensins with a similar arrangement of cysteine residues. Ensuing studies demonstrated that PPAF-II forms a homo-oligomer upon cleavage by the upstream protease and that the clip domain of PPAF-II functions as a module for binding phenoloxidase through the central cleft, while the clip domain of a catalytically active easter-type SP plays an essential role in the rapid activation of its protease domain.


    Organizational Affiliation

    National Research Laboratory of Defense Proteins, College of Pharmacy and Research Institute for Drug Development, Pusan National University, Jangjeon Dong, Geumjeong Gu, Busan, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
prophenoloxidase activating factor
A
394Holotrichia diomphaliaMutation(s): 0 
Gene Names: PPAF2 (PPAF-II)
Find proteins for Q9GRW0 (Holotrichia diomphalia)
Go to UniProtKB:  Q9GRW0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.780α = 90.00
b = 76.587β = 113.45
c = 69.833γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance