1P04

STRUCTURE ANALYSIS OF SPECIFICITY. ALPHA-LYTIC PROTEASE COMPLEXES WITH ANALOGUES OF REACTION INTERMEDIATES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of specificity: alpha-lytic protease complexes with analogues of reaction intermediates.

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

(1989) Biochemistry 28: 7600-7609

  • Primary Citation of Related Structures:  1P02, 1P03, 1P05, 1P06

  • PubMed Abstract: 
  • To better understand the structural basis of enzyme specificity, the structures of complexes formed between alpha-lytic protease, an extracellular serine protease of Lysobacter enzymogenes, and five inhibitory peptide boronic acids (R2-boroX, where R ...

    To better understand the structural basis of enzyme specificity, the structures of complexes formed between alpha-lytic protease, an extracellular serine protease of Lysobacter enzymogenes, and five inhibitory peptide boronic acids (R2-boroX, where R2 is methoxysuccinyl-Ala-Ala-Pro- and boroX is the alpha-aminoboronic acid analogue of Ala, Val, Ile, Norleu, or Phe) have been studied at high resolution by X-ray crystallography. The enzyme has primary specificity for Ala in the P1 position of peptide substrates with catalytic efficiency decreasing with increasing side-chain volume. Enzyme affinity for inhibitors with boroVal, boroIle, and boroPhe residues is much higher than expected on the basis of the catalytic efficiencies of homologous substrates. Covalent tetrahedral adducts are formed between the active-site serine and the boronic acid moieties of R2-boroAla, R2-boroVal R2-boroIle, and R2-boroNorleu. Though R2-boroVal is a slowly bound inhibitor and R2-boroAla is rapidly bound [Kettner, C. A., Bone, R., Agard, D. A., & Bachovchin, W. W. (1988) Biochemistry 27, 7682-7688], there appear to be no structural differences that could account for slow binding. The removal from solution of 20% more hydrophobic surface on binding accounts for the improved affinity of alpha-lytic protease for R2-boroVal relative to R2-boroAla. The high affinity of the enzyme for R2-boroIle derives from the selective binding of the L-allo stereoisomer of the boroIle residue, which can avoid bad steric interactions in the binding pocket.(ABSTRACT TRUNCATED AT 250 WORDS)


    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
    • 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
    • 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
    • Structural Plasticity as a Determinant of Enzyme Specificity. Creating Broadly Specific Proteases
      Bone, R.,Silen, J.L.,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


    Organizational Affiliation

    Department of Biochemistry and 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
METHOXYSUCCINYL-ALA-ALA-PRO-ISOLEUCINE BORONIC ACID INHIBITOR
P
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000313
Query on PRD_000313
PMeOSuc-Ala-Ala-Pro-boroIlePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.300α = 90.00
b = 66.300β = 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: 2008-03-25
    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