1P01

Serine protease mechanism. structure of an inhibitory complex oF ALPHA-LYTIC Protease and a tightly bound peptide boronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 7609-7614


  • PubMed Abstract: 
  • The structure of the complex formed between alpha-lytic protease, a serine protease secreted by Lysobacter enzymogenes, and N-tert-butyloxycarbonylalanylprolylvaline boronic acid (Ki = 0.35 nM) has been studied by X-ray crystallography to a resolutio ...

    The structure of the complex formed between alpha-lytic protease, a serine protease secreted by Lysobacter enzymogenes, and N-tert-butyloxycarbonylalanylprolylvaline boronic acid (Ki = 0.35 nM) has been studied by X-ray crystallography to a resolution of 2.0 A. The active-site serine forms a covalent, nearly tetrahedral adduct with the boronic acid moiety of the inhibitor. The complex is stabilized by seven hydrogen bonds between the enzyme and inhibitor with additional stabilization arising from van der Waals interactions between enzyme and inhibitor side chains and the burying of 330 A2 of hydrophobic surface area. Hydrogen bonding between Asp-102 and His-57 remains intact in the enzyme-inhibitor complex, and His N epsilon 2 is well positioned to donate its hydrogen to the leaving group. Little change in the positions of protease residues was observed on complex formation (root mean square main chain deviation = 0.13 A), suggesting that in its native state the enzyme is complementary to tetrahedral reaction intermediates or to the nearly tetrahedral transition state for the reaction.


    Related Citations: 
    • 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
    • Structural Plasticity as a Determinant of Enzyme Specificity. Creating Broadly Specific Proteases
      Bone, R.,Silen, J.L.,Agard, D.A.
      () TO BE PUBLISHED --: --
    • Structure Analysis of Specificity. Alpha-Lytic Protease Complexes with Analogs of Reaction Intermediates
      Bone, R.,Frank, D.,Kettner, C.,Agard, D.A.
      () TO BE PUBLISHED --: --
    • 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
    • Kinetic Properties of the Binding of Alpha-Lytic Protease to Peptide Boronic Acids
      Kettner, C.A.,Bone, R.,Agard, D.A.,Bachovchin, W.W.
      (1988) Biochemistry 27: 7682


    Organizational Affiliation

    Department of Biochemistry & Biophysics, University of California, San Francisco 94143-0448.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-LYTIC PROTEASE
A
198Lysobacter enzymogenesGene Names: alpha-LP
EC: 3.4.21.12
Find proteins for P00778 (Lysobacter enzymogenes)
Go to UniProtKB:  P00778
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
0EG
Query on 0EG

Download SDF File 
Download CCD File 
A
N-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(dihydroxyboranyl)-2-methylpropyl]-L-prolinamide
N-tert-butyloxycarbonylalanylprolylvaline boronic acid
C17 H32 B N3 O6
VWVBZPYREZAAER-AVGNSLFASA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000261 (0EG)
Query on PRD_000261
AN-(tert-butoxycarbonyl)-L-alanyl-N-[(1R)-1-(dihydroxyboranyl)-2-methylpropyl]-L-prolinamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.340α = 90.00
b = 66.340β = 90.00
c = 80.310γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1989-04-24 
  • Released Date: 1990-04-15 
  • Deposition Author(s): Bone, R., Agard, D.A.

Revision History 

  • Version 1.0: 1990-04-15
    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