1ST2

THE THREE-DIMENSIONAL STRUCTURE OF BACILLUS AMYLOLIQUEFACIENS SUBTILISIN AT 1.8 ANGSTROMS AND AN ANALYSIS OF THE STRUCTURAL CONSEQUENCES OF PEROXIDE INACTIVATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The three-dimensional structure of Bacillus amyloliquefaciens subtilisin at 1.8 A and an analysis of the structural consequences of peroxide inactivation.

Bott, R.Ultsch, M.Kossiakoff, A.Graycar, T.Katz, B.Power, S.

(1988) J Biol Chem 263: 7895-7906

  • Primary Citation of Related Structures:  
    2ST1, 1ST2

  • PubMed Abstract: 
  • The three-dimensional structure of the subtilisin from Bacillus amyloliquefaciens (BAS) has been refined to 1.8 A using the amino acid sequence deduced from the DNA coding sequence. The structure is essentially the same as the previously reported structures of subtilisin BPN' (Wright, C ...

    The three-dimensional structure of the subtilisin from Bacillus amyloliquefaciens (BAS) has been refined to 1.8 A using the amino acid sequence deduced from the DNA coding sequence. The structure is essentially the same as the previously reported structures of subtilisin BPN' (Wright, C.S., Alden, R.A., and Kraut, J. (1969) Nature 221, 235-242) and Novo (Drenth, J., Hol, W. G. J., Jansonius, J. N., and Koekoek, R. (1972) Eur. J. Biochem. 26, 177-181) determined in different crystal forms, at 2.5 and 2.8 A resolution, respectively. The largest differences in the three crystallographic models are seen in regions where the amino acid sequence used in the fit to the electron density maps of BPN' and Novo differs from the gene sequence of BAS (Wells, J. A., Ferrari, E., Henner, D. J., Estell, D. A., and Chen, E. Y. (1983) Nucleic Acids Res. 11, 7911-7925). The refined BAS model shows new features of cation binding, hydrogen bonding, and internal solvent structure. The refined BAS model has served as a basis for the analysis of stereochemical factors involved in the peroxide inactivation of the enzyme. Methionine 222, which is adjacent to the catalytic Ser221, is quantitatively oxidized to the sulfoxide by hydrogen peroxide as had been previously shown for the related Bacillus licheniformis enzyme (Stauffer, C. E., and Etson, D. (1969) J. Biol. Chem. 244, 5333-5338). In addition to this site of modification, we observe partial to full oxidation of two of the four remaining methionines. The oxidation of the methionines does not correlate well with their solvent accessibility calculated from the x-ray structure coordinates; in addition, only one of the two possible stereoisomers of methionine sulfoxide is formed. We also detect hydrogen peroxide-induced modification of the hydroxyl groups of two tyrosines. Modeling suggests that most of the observed effect of oxidation on the enzyme's catalytic efficiency can be attributed to unfavorable interactions at the oxyanion binding site between the sulfoxide group at 222 and the carbonyl oxygen of the scissile peptide bond of the bound substrate.


    Related Citations: 
    • Cloning, Sequencing and Secretion of Bacillus Amyloliquefaciens Subtilisin in Bacillus Subtilis
      Wells, J.A., Ferrari, E., Henner, D.J., Estell, D.A., Chen, E.Y.
      (1983) Nucleic Acids Res 11: 7911

    Organizational Affiliation

    Department of Biomolecular Chemistry, Genentech, Inc., South San Francisco, California 94080.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUBTILISIN BPN' A275Bacillus amyloliquefaciensMutation(s): 0 
Gene Names: apr
EC: 3.4.21.14 (PDB Primary Data), 3.4.21.62 (UniProt)
Find proteins for P00782 (Bacillus amyloliquefaciens)
Explore P00782 
Go to UniProtKB:  P00782
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MHO
Query on MHO
AL-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.3α = 90
b = 72.8β = 90
c = 75.35γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1990-03-21 
  • Released Date: 1991-07-15 
  • Deposition Author(s): Bott, R.

Revision History  (Full details and data files)

  • Version 1.0: 1991-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance