3I74 | pdb_00003i74

Crystal Structure of the plant subtilisin-like protease SBT3 in complex with a chloromethylketone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.294 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 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 U S A 106: 17223-17228

  • DOI: https://doi.org/10.1073/pnas.0907587106
  • Primary Citation Related Structures: 
    3I6S, 3I74

  • 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, 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.

Macromolecule Content 

  • Total Structure Weight: 143.48 kDa 
  • Atom Count: 10,391 
  • Modeled Residue Count: 1,294 
  • Deposited Residue Count: 1,310 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Subtilisin-like protease
A, B
649Solanum lycopersicumMutation(s): 0 
EC: 3.4.21
UniProt
Find proteins for O82777 (Solanum lycopersicum)
Explore O82777 
Go to UniProtKB:  O82777
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO82777
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ACE-PHE-GLU-LYS-ALA chloromethylketone INHIBITOR
C, D
6N/AMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
F, G, I, J
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G11971MR
GlyCosmos: G11971MR
GlyGen: G11971MR
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G80587NA
GlyCosmos: G80587NA
GlyGen: G80587NA

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALV
Query on ALV
C, D
PEPTIDE-LIKEC3 H9 N O2ALA

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.294 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.73α = 90
b = 143.73β = 90
c = 195.19γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary