1SIP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.170 

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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
  • Primary Citation of Related Structures:  
    1SIP

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UNLIGANDED SIV PROTEASEA99Simian immunodeficiency virusMutation(s): 0 
Gene Names: pol
EC: 3.4.23 (PDB Primary Data), 2.7.7.49 (UniProt), 3.1.13.2 (UniProt), 3.1.26.13 (UniProt)
Find proteins for Q88016 (Simian immunodeficiency virus)
Explore Q88016 
Go to UniProtKB:  Q88016
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.18α = 90
b = 62.52β = 90
c = 95.76γ = 90
Software Package:
Software NamePurpose
RESTRAINrefinement
FRODOmodel building

Structure Validation

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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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance