Experimental Data Snapshot

  • Resolution: 2.15 Å

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural basis for broad specificity in alpha-lytic protease mutants.

Bone, R.Fujishige, A.Kettner, C.A.Agard, D.A.

(1991) Biochemistry 30: 10388-10398

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Binding pocket mutants of alpha-lytic protease (Met 192----Ala and Met 213----Ala) have been constructed recently in an effort to create a protease specific for Met just prior to the scissile bond. Instead, mutation resulted in proteases with extraor ...

    Binding pocket mutants of alpha-lytic protease (Met 192----Ala and Met 213----Ala) have been constructed recently in an effort to create a protease specific for Met just prior to the scissile bond. Instead, mutation resulted in proteases with extraordinarily broad specificity profiles and high activity [Bone, R., Silen, J. L., & Agard, D. A. (1989) Nature 339, 191-195]. To understand the structural basis for the unexpected specificity profiles of these mutants, high-resolution X-ray crystal structures have been determined for complexes of each mutant with a series of systematically varying peptidylboronic acids. These inhibitory analogues of high-energy reaction intermediates provide models for how substrates with different side chains interact with the enzyme during the transition state. Fifteen structures have been analyzed qualitatively and quantitatively with respect to enzyme-inhibitor hydrogen-bond lengths, buried hydrophobic surface area, unfilled cavity volume, and the magnitude of inhibitor accommodating conformational adjustments (particularly in the region of another binding pocket residue, Val 217A). Comparison of these four parameters with the Ki of each inhibitor and the kcat and Km of the analogous substrates indicates that while no single structural parameter consistently correlates with activity or inhibition, the observed data can be understood as a combination of effects. Furthermore, the relative contribution of each term differs for the three enzymes, reflecting the altered conformational energetics of each mutant. From the extensive structural analysis, it is clear that enzyme flexibility, especially in the region of Val 217A, is primarily responsible for the exceptionally broad specificity observed in either mutant. Taken together, the observed patterns of substrate specificity can be understood to arise directly from interactions between the substrate and the residues lining the specificity pocket and indirectly from interactions between peripheral regions of the protein and the active-site region that serve to modulate active-site flexibility.

    Related Citations: 
    • Serine Protease Mechanism: Structure of an Inhibitory Complex of Alpha-Lytic Protease and a Tightly Bound Peptide Boronic Acid
      Bone, R.,Shenvi, A.B.,Kettner, C.A.,Agard, D.A.
      (1987) Biochemistry 26: 7609
    • Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution. Analysis of Hydrogen Bonding and Solvent Structure
      Fujinaga, M.,Delbaere, L.T.J.,Brayer, G.D.,James, M.N.G.
      (1985) J.Mol.Biol. 184: 479
    • Structural Plasticity Broadens the Specificity of an Engineered Protease
      Bone, R.,Silen, J.L.,Agard, D.A.
      (1989) Nature 339: 191
    • Structural Analysis of Specificity: Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates
      Bone, R.,Frank, D.,Kettner, D.,Agard, D.A.
      (1989) Biochemistry 28: 7600
    • Kinetic Properties of the Binding of Alpha-Lytic Protease to Peptide Boronic Acids
      Kettner, D.A.,Bone, R.,Agard, D.A.,Bachovchin, W.W.
      (1988) Biochemistry 27: 7682
    • Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution
      Brayer, G.D.,Delbaere, L.T.J.,James, M.N.G.
      (1979) J.Mol.Biol. 131: 743

    Organizational Affiliation

    Department of Biochemistry, Howard Hughes Medical Institute, University of California, San Francisco 94143-0448.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
198Lysobacter enzymogenesMutation(s): 0 
Gene Names: alpha-LP
Find proteins for P00778 (Lysobacter enzymogenes)
Go to UniProtKB:  P00778
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download SDF File 
Download CCD File 
O4 S
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
Query on PRD_000318
PN-(4-methoxy-4-oxobutanoyl)-L-alanyl-L-alanyl-N-[(1R)-1-(dihydroxyboranyl)pentyl]-L-prolinamidePeptide-like / Inhibitor


Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.370α = 90.00
b = 66.370β = 90.00
c = 80.100γ = 120.00
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

  • Deposited Date: 1991-08-05 
  • Released Date: 1993-01-15 
  • Deposition Author(s): Bone, R., Agard, D.A.

Revision History 

  • Version 1.0: 1993-01-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other