2NPH

Crystal structure of HIV1 protease in situ product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of HIV-1 protease in situ product complex and observation of a low-barrier hydrogen bond between catalytic aspartates

Das, A.Prashar, V.Mahale, S.Serre, L.Ferrer, J.-L.Hosur, M.V.

(2006) Proc.Natl.Acad.Sci.Usa 103: 18464-18469

  • DOI: 10.1073/pnas.0605809103
  • Also Cited By: 3DOX

  • PubMed Abstract: 
  • HIV-1 protease is an effective target for designing drugs against AIDS, and structural information about the true transition state and the correct mechanism can provide important inputs. We present here the three-dimensional structure of a bi-product ...

    HIV-1 protease is an effective target for designing drugs against AIDS, and structural information about the true transition state and the correct mechanism can provide important inputs. We present here the three-dimensional structure of a bi-product complex between HIV-1 protease and the two cleavage product peptides AETF and YVDGAA. The structure, refined against synchrotron data to 1.65 A resolution, shows the occurrence of the cleavage reaction in the crystal, with the product peptides still held in the enzyme active site. The separation between the scissile carbon and nitrogen atoms is 2.67 A, which is shorter than a normal van der Waal separation, but it is much longer than a peptide bond length. The substrate is thus in a stage just past the G'Z intermediate described in Northrop's mechanism [Northrop DB (2001) Acc Chem Res 34:790-797]. Because the products are generated in situ, the structure, by extrapolation, can give insight into the mechanism of the cleavage reaction. Both oxygens of the generated carboxyl group form hydrogen bonds with atoms at the catalytic center: one to the OD2 atom of a catalytic aspartate and the other to the scissile nitrogen atom. The latter hydrogen bond may have mediated protonation of scissile nitrogen, triggering peptide bond cleavage. The inner oxygen atoms of the catalytic aspartates in the complex are 2.30 A apart, indicating a low-barrier hydrogen bond between them at this stage of the reaction, an observation not included in Northrop's proposal. This structure forms a template for designing mechanism-based inhibitors.


    Related Citations: 
    • Observation of a tetrahedral reaction intermediate in HIV-1 protease substrate complex
      Kumar, M.,Prashar, V.,Mahale, S.,V., Hosur M.
      (2005) Biochem.J. 389: 365
    • Effects of remote mutation on the autolysis of HIV-1 PR: X-ray and NMR investigations
      Kumar, M.,Kannan, K.K.,Hosur, M.V.,Bhavesh, N.S.,Chatterjee, A.,Mittal, R.,Hosur, R.V.
      (2002) Biochem.Biophys.Res.Commun. 294: 395
    • 1.9A X-ray study shows closed flap conformation in crystals of tethered HIV-1 PR
      Pillai, B.,Kannan, K.K.,Hosur, M.V.
      (2001) Proteins 43: 57
    • Rapid screening for HIV-1 protease inhibitor leads through X-ray diffraction
      Pillai, B.,Bhat, S.V.,Kannan, K.K.,Hosur, M.V.
      (2004) Acta Crystallogr.,Sect.D 60: 594


    Organizational Affiliation

    Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASE RETROPEPSIN
A, B
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
tetrapeptide fragment
S
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
pentapeptide fragment
T
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.030α = 90.00
b = 62.030β = 90.00
c = 81.780γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description