3I6S

Crystal Structure of the plant subtilisin-like protease SBT3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for Ca2+-independence and activation by homodimerization of tomato subtilase 3.

Ottmann, C.Rose, R.Huttenlocher, F.Cedzich, A.Hauske, P.Kaiser, M.Huber, R.Schaller, A.

(2009) Proc.Natl.Acad.Sci.USA 106: 17223-17228

  • DOI: 10.1073/pnas.0907587106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Subtilases are serine proteases found in Archae, Bacteria, yeasts, and higher eukaryotes. Plants possess many more of these subtilisin-like endopeptidases than animals, e.g., 56 identified genes in Arabidopsis compared with only 9 in humans, indicati ...

    Subtilases are serine proteases found in Archae, Bacteria, yeasts, and higher eukaryotes. Plants possess many more of these subtilisin-like endopeptidases than animals, e.g., 56 identified genes in Arabidopsis compared with only 9 in humans, indicating important roles for subtilases in plant biology. We report the first structure of a plant subtilase, SBT3 from tomato, in the active apo form and complexed with a chloromethylketone (cmk) inhibitor. The domain architecture comprises an N-terminal protease domain displaying a 132 aa protease-associated (PA) domain insertion and a C-terminal seven-stranded jelly-roll fibronectin (Fn) III-like domain. We present the first structural evidence for an explicit function of PA domains in proteases revealing a vital role in the homo-dimerization of SBT3 and in enzyme activation. Although Ca(2+)-binding sites are conserved and critical for stability in other subtilases, SBT3 was found to be Ca(2+)-free and its thermo stability is Ca(2+)-independent.


    Organizational Affiliation

    Chemical Genomics Centre, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Subtilisin-like protease
A, B
649Solanum lycopersicumMutation(s): 0 
Gene Names: sbt3
EC: 3.4.21.-
Find proteins for O82777 (Solanum lycopersicum)
Go to UniProtKB:  O82777
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.249 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 143.890α = 90.00
b = 143.890β = 90.00
c = 195.140γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-07-07 
  • Released Date: 2010-01-19 
  • Deposition Author(s): Rose, R., Ottmann, C.

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance