1P12

CRYSTAL STRUCTURES OF ALPHA-LYTIC PROTEASE COMPLEXES WITH IRREVERSIBLY BOUND PHOSPHONATE ESTERS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of alpha-lytic protease complexes with irreversibly bound phosphonate esters.

Bone, R.Sampson, N.S.Bartlett, P.A.Agard, D.A.

(1991) Biochemistry 30: 2263-2272

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of the complexes with alpha-lytic protease of both phosphorus stereoisomers of N-[(2S)-2-[[[(1R)-1-[N-[(tert-butyloxycarbonyl)-L-alanyl-L-alanyl- L-prolyl]amino]-2-methylpropyl]-phenoxyphosphinyl]oxy]propanoyl]- L-alanine methyl ester, ...

    The structures of the complexes with alpha-lytic protease of both phosphorus stereoisomers of N-[(2S)-2-[[[(1R)-1-[N-[(tert-butyloxycarbonyl)-L-alanyl-L-alanyl- L-prolyl]amino]-2-methylpropyl]-phenoxyphosphinyl]oxy]propanoyl]- L-alanine methyl ester, an analogue of the peptide Boc-Ala-Ala-Pro-Val-Ala-Ala where Val is replaced with an analogous phosphonate phenyl ester and the subsequent Ala is replaced with lactate, have been determined to high resolution (1.9 A) by X-ray crystallography. Both stereoisomers inactivate the enzyme but differ by a factor of 2 in the second-order rate constant for inactivation [Sampson, N. S., & Bartlett, P. A. (1991) Biochemistry (preceding paper in this issue)]. One isomer (B) forms a tetrahedral adduct in which the phosphonate phenyl ester is displaced by the active site serine (S195) and interacts with the enzyme across seven substrate recognition sites that span both sides of the scissile bond. Seven hydrogen bonds are formed with the enzyme, and 510 A2 of hydrophobic surface area is buried when the inhibitor interacts with the enzyme. Although two hydrogen bonds are gained by incorporation of two residues on the C-terminal side of the scissile bond into the inhibitor, there is very little adjustment in the structure of the enzyme in this region. Surprisingly, the active site histidine (H57) does not interact with the phosphonate, apparently because the phosphonate lacks negative charge in or near the oxyanion hole, and instead, the side chain rotates out of the active site cleft and hydrogen bonds with solvent. The other isomer (A) forms a mixture of two different tetrahedral adducts in the active site, both covalently bonded to Ser 195. One adduct, at approximately 58% occupancy, is exactly the same in structure as the complex formed with isomer B, and the other adduct, at 42% occupancy, has lost the two residues C-terminal to the scissile bond by hydrolysis. In the lower occupancy structure, His 57 does not rotate out of the active site and forms a hydrogen bond with the phosphonate oxygen instead. The structures of both complexes were insensitive to pH. As very little change in structure accompanies the histidine rotation, the complex with isomer B provides an excellent mimic for the structure of the transition state (or high-energy reaction intermediate) that spans both sides of the scissile bond.


    Related Citations: 
    • 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. 131: 479
    • 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: 643
    • Peptidic Phosphonylating Agents as Irreversible Inhibitors of Serine Proteases and Models of the Tetrahedral Intermediates
      Sampson, N.S.,Bartlett, P.A.
      (1991) Biochemistry 30: 2255


    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
E
198Lysobacter enzymogenesMutation(s): 0 
Gene Names: alpha-LP
EC: 3.4.21.12
Find proteins for P00778 (Lysobacter enzymogenes)
Go to UniProtKB:  P00778
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOSPHONATE ESTER INHIBITOR
I
7N/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
SO4
Query on SO4

Download SDF File 
Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 66.790α = 90.00
b = 66.790β = 90.00
c = 79.900γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1990-10-26 
  • 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: 2008-03-24
    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