1BH6

SUBTILISIN DY IN COMPLEX WITH THE SYNTHETIC INHIBITOR N-BENZYLOXYCARBONYL-ALA-PRO-PHE-CHLOROMETHYL KETONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Observed: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of subtilisin DY, a random mutant of subtilisin Carlsberg.

Eschenburg, S.Genov, N.Peters, K.Fittkau, S.Stoeva, S.Wilson, K.S.Betzel, C.

(1998) Eur J Biochem 257: 309-318

  • DOI: 10.1046/j.1432-1327.1998.2570309.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of subtilisin DY inhibited by N-benzyloxycarbonyl-Ala-Pro-Phe-chloromethyl ketone has been solved by molecular replacement with subtilisin Carlsberg as the starting model. The model has been refined to a crystallographic R facto ...

    The crystal structure of subtilisin DY inhibited by N-benzyloxycarbonyl-Ala-Pro-Phe-chloromethyl ketone has been solved by molecular replacement with subtilisin Carlsberg as the starting model. The model has been refined to a crystallographic R factor (= sigma absolute value [(absolute value Fo) - (absolute value Fc)] / sigma (absolute value of Fo) of 15.1% using X-ray diffraction data to 0.175 nm resolution. Subtilisin DY is an alkaline proteinase from the X-irradiated Japanese strain DY of Bacillus licheniformis, which normally produces subtilisin Carlsberg. It has very similar properties to subtilisin Carlsberg, with a slightly enhanced resistance to heat and guanidine hydrochloride-induced denaturation, in spite of the fact that the sequences of the two enzymes differ in 31 positions out of 274 residues. The close similarity in overall three-dimensional structure of subtilisins DY and Carlsberg and also their physicochemical properties, such as activity and stability, shows that nature aided by X-irradiation for rapid 'evolution' is able to accommodate considerable changes in sequence without substantial changes in property.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Subtilisin Dy, a Natural Mutant of Subtilisin Carlsberg
      Betzel, C., Visanji, M., Eschenburg, S., Wilson, K.S., Peters, K., Fittkau, S., Singh, T.P., Genov, N.
      (1993) Arch Biochem Biophys 302: 499

    Organizational Affiliation

    European Molecular Biology Laboratory, Institute of Physiological Chemistry, Hamburg, Germany. Susanna@unisgi1.desy.de



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUBTILISIN DYA274Bacillus licheniformisMutation(s): 0 
Gene Names: apr
EC: 3.4.21.62
Find proteins for P00781 (Bacillus licheniformis)
Explore P00781 
Go to UniProtKB:  P00781
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1BH
Query on 1BH

Download CCD File 
A
N-BENZYLOXYCARBONYL-ALA-PRO-3-AMINO-4-PHENYL-BUTAN-2-OL
C26 H33 N3 O5
MACLRJNEKXUAJK-YDLSIGKMSA-N
 Ligand Interaction
CA
Query on CA

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

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.83α = 90
b = 72.75β = 90
c = 59.89γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance