Alpha-lytic protease with met 190 replaced by ALA AND GLY 216 replaced by ALA complex with METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity.

Mace, J.E.Agard, D.A.

(1995) J.Mol.Biol. 254: 720-736

  • DOI: 10.1006/jmbi.1995.0650
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gly216 in the active site of the broadly specific MA190 mutant of alpha-lytic protease has been found to be remarkably tolerant of amino acid substitutions. Side-chains as large as Trp can be accommodated within the substrate-binding pocket without a ...

    Gly216 in the active site of the broadly specific MA190 mutant of alpha-lytic protease has been found to be remarkably tolerant of amino acid substitutions. Side-chains as large as Trp can be accommodated within the substrate-binding pocket without abolishing catalysis, and have major effects upon the substrate specificity of the enzyme. Kinetic characterization of eleven enzymatically active mutants against a panel of eight substrates clearly revealed the functional consequences of the substitutions at position 216. To understand better the structural basis for their altered specificity, the GA216 + MA190 and GL216 + MA190 mutants have been crystallized both with and without a representative series of peptide boronic acid transition-state analog inhibitors. An empirical description and non-parametric statistical analysis of structural variation among these enzyme: inhibitor complexes is presented. The roles of active site plasticity and dynamics in alpha-lytic protease function and substrate preference are also addressed. The results strongly suggest that substrate specificity determination in alpha-lytic protease is a distributed property of the active site and substrate molecule.

    Related Citations: 
    • Structural Basis for Broad Specificity in Alpha-Lytic Protease
      Bone, R.,Fujushige, A.,Kettner, C.A.,Agard, D.A.
      (1991) Biochemistry 30: 10388
    • 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
    • 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
    • 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 27: 7609
    • 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

    Organizational Affiliation

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


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
198Lysobacter enzymogenesMutation(s): 2 
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_000314


Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Work: 0.142 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.200α = 90.00
b = 66.200β = 90.00
c = 80.090γ = 120.00
Software Package:
Software NamePurpose
RIGAKUdata reduction
RIGAKUdata collection
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    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