1SIP

ALTERNATIVE NATIVE FLAP CONFORMATION REVEALED BY 2.3 ANGSTROMS RESOLUTION STRUCTURE OF SIV PROTEINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Alternative native flap conformation revealed by 2.3 A resolution structure of SIV proteinase.

Wilderspin, A.F.Sugrue, R.J.

(1994) J.Mol.Biol. 239: 97-103

  • DOI: 10.1006/jmbi.1994.1353

  • PubMed Abstract: 
  • A large conformational change is observed between HIV-1 proteinase in the ligand-free state and in complexes with transition-state inhibitors. Crystal structures of this enzyme have either the flaps open for the native or ligand-free enzyme or the fl ...

    A large conformational change is observed between HIV-1 proteinase in the ligand-free state and in complexes with transition-state inhibitors. Crystal structures of this enzyme have either the flaps open for the native or ligand-free enzyme or the flaps closed for peptidomimetic ligand-bound enzyme. We describe the structure of native recombinant SIV proteinase which like other retroviral proteinases crystallizes as a perfect 2-fold symmetric dimer but in a different crystal packing arrangement. In contrast to HIV-1 PR we show that SIV proteinase in the ligand-free state adopts the closed flaps conformation, demonstrating that ligand binding is not a prerequisite for the closed flaps conformation. The catalytic water was clearly observed between the two aspartates which were not perfectly co-planar, and in this structure the active site cleft is more restricted than for either inhibitor bound or ligand-free HIV-1 proteinase. Accommodation of two bulkier side-chains in the simian enzyme core has resulted in a more exposed N terminus than for HIV-1 PR which we predict could enhance autocatalytic cleavage at the N terminus.


    Related Citations: 
    • Purification of Crystallizable Recombinant Sivmac251-32H Proteinase
      Sugrue, R.J.,Almond, N.,Kitchin, P.,Richardson, S.M.H.,Wilderspin, A.F.
      (1994) Protein Expr.Purif. 5: 76
    • Crystallization and Preliminary X-Ray Investigation of Recombinant Simian Immunodeficiency Virus Proteinase
      Wilderspin, A.F.,Sugrue, R.J.
      (1993) J.Mol.Biol. 231: 1139


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, London, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UNLIGANDED SIV PROTEASE
A
99Simian immunodeficiency virus (isolate mac239)Mutation(s): 0 
Gene Names: pol
Find proteins for Q88016 (Simian immunodeficiency virus (isolate mac239))
Go to UniProtKB:  Q88016
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 32.180α = 90.00
b = 62.520β = 90.00
c = 95.760γ = 90.00
Software Package:
Software NamePurpose
RESTRAINrefinement
FRODOmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-04-13 
  • Released Date: 1994-08-31 
  • Deposition Author(s): Wilderspin, A.F.

Revision History 

  • Version 1.0: 1994-08-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance