1AZ5

UNLIGANDED SIV PROTEASE STRUCTURE IN AN "OPEN" CONFORMATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Domain flexibility in retroviral proteases: structural implications for drug resistant mutations.

Rose, R.B.Craik, C.S.Stroud, R.M.

(1998) Biochemistry 37: 2607-2621

  • DOI: 10.1021/bi9716074

  • PubMed Abstract: 
  • Rigid body rotation of five domains and movements within their interfacial joints provide a rational context for understanding why HIV protease mutations that arise in drug resistant strains are often spatially removed from the drug or substrate bind ...

    Rigid body rotation of five domains and movements within their interfacial joints provide a rational context for understanding why HIV protease mutations that arise in drug resistant strains are often spatially removed from the drug or substrate binding sites. Domain motions associated with substrate binding in the retroviral HIV-1 and SIV proteases are identified and characterized. These motions are in addition to closure of the flaps and result from rotations of approximately 6-7 degrees at primarily hydrophobic interfaces. A crystal structure of unliganded SIV protease (incorporating the point mutation Ser 4 His to stabilize the protease against autolysis) was determined to 2.0 A resolution in a new space group, P3221. The structure is in the most "open" conformation of any retroviral protease so far examined, with six residues of the flaps disordered. Comparison of this and unliganded HIV structures, with their respective liganded structures by difference distance matrixes identifies five domains of the protease dimer that move as rigid bodies against one another: one terminal domain encompassing the N- and C-terminal beta sheet of the dimer, two core domains containing the catalytic aspartic acids, and two flap domains. The two core domains rotate toward each other on substrate binding, reshaping the binding pocket. We therefore show that, for enzymes, mutations at interdomain interfaces that favor the unliganded form of the target active site will increase the off-rate of the inhibitor, allowing the substrate greater access for catalysis. This offers a mechanism of resistance to competitive inhibitors, especially when the forward enzymatic reaction rate exceeds the rate of substrate dissociation.


    Related Citations: 
    • Three-Dimensional Structures of HIV-1 and Siv Protease Product Complexes
      Rose, R.B.,Craik, C.S.,Douglas, N.L.,Stroud, R.M.
      (1996) Biochemistry 35: 12933


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California in San Francisco, San Francisco, California 94143-0448, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIV PROTEASE
A
99Simian immunodeficiency virusMutation(s): 1 
Gene Names: gag-pol
Find proteins for P05896 (Simian immunodeficiency virus)
Go to UniProtKB:  P05896
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 45.400α = 90.00
b = 45.400β = 90.00
c = 87.900γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model