3BGO

Azide complex of Engineered Subtilisin SUBT_BACAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a switchable subtilisin complexed with a substrate and with the activator azide.

Gallagher, T.Ruan, B.London, M.Bryan, M.A.Bryan, P.N.

(2009) Biochemistry 48: 10389-10394

  • DOI: 10.1021/bi900577n
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An engineered variant of the protease subtilisin from Bacillus amyloliquefaciens, in which the D32A mutation renders the enzyme's activity dependent on the presence of certain small anions such as fluoride or azide, has been produced. This modified e ...

    An engineered variant of the protease subtilisin from Bacillus amyloliquefaciens, in which the D32A mutation renders the enzyme's activity dependent on the presence of certain small anions such as fluoride or azide, has been produced. This modified enzyme has applications as an azide or fluoride-triggered expression-purification tool. We report activity measurements showing that the enzyme is activated more than 3000-fold by azide and describe the 1.8 A resolution structure of an inactive form (by replacing the catalytic nucleophile Ser 221 with alanine) of the protease, in complex with azide and with a substrate that spans the active site. Both enzyme and substrate have been engineered to increase their stability and the affinity of their interaction. The substrate is based on a stabilized subtilisin prodomain, extended across the active site by the addition of four residues at its C-terminus. In the crystal structure, the substrate is well-ordered across the active site, and the azide anion is observed bound adjacent to Ala 32. The structures of the substrate complex in three different crystals (anion-free, fluoride-soaked, and azide-soaked) are compared. These structures provide extensive information for understanding subtilisin's substrate binding and catalytic mechanism, and for the development of biotechnology tools based on anion-activated proteolysis. The mechanism of anion-dependent proteolysis appears to be a slight modification of the accepted charge-relay mechanism for serine proteases.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA. gallaghe@umbi.umd.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Subtilisin BPN'
P
80Bacillus amyloliquefaciensMutation(s): 9 
Gene Names: apr
EC: 3.4.21.62
Find proteins for P00782 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P00782
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Subtilisin BPN'
S
266Bacillus amyloliquefaciensMutation(s): 22 
Gene Names: apr
EC: 3.4.21.62
Find proteins for P00782 (Bacillus amyloliquefaciens)
Go to UniProtKB:  P00782
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
S
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

Download SDF File 
Download CCD File 
S
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.290α = 90.00
b = 72.840β = 90.00
c = 95.020γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2016-11-02
    Type: Database references