6S1V

Crystal structure of dimeric M-PMV protease D26N mutant in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report



Literature

Comparison of a retroviral protease in monomeric and dimeric states.

Wosicki, S.Gilski, M.Zabranska, H.Pichova, I.Jaskolski, M.

(2019) Acta Crystallogr D Struct Biol 75: 904-917

  • DOI: 10.1107/S2059798319011355
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a w ...

    Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason-Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 Å, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S-S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.


    Related Citations: 
    • Crystal structure of a monomeric retroviral protease solved by protein folding game players.
      Khatib, F., DiMaio, F., Cooper, S., Kazmierczyk, M., Gilski, M., Krzywda, S., Zabranska, H., Pichova, I., Thompson, J., Popovic, Z., Jaskolski, M., Baker, D.
      (2011) Nat Struct Mol Biol 18: 1175
    • High-resolution structure of a retroviral protease folded as a monomer.
      Gilski, M., Kazmierczyk, M., Krzywda, S., Zabranska, H., Cooper, S., Popovic, Z., Khatib, F., DiMaio, F., Thompson, J., Baker, D., Pichova, I., Jaskolski, M.
      (2011) Acta Crystallogr D Biol Crystallogr 67: 907
    • Crystal structure of a retroviral protease proves relationship to aspartic protease family.
      Miller, M., Jaskolski, M., Rao, J.K., Leis, J., Wlodawer, A.
      (1989) Nature 337: 576
    • Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease.
      Wlodawer, A., Miller, M., Jaskolski, M., Sathyanarayana, B.K., Baldwin, E., Weber, I.T., Selk, L.M., Clawson, L., Schneider, J., Kent, S.B.
      (1989) Science 245: 616

    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pro-Pol polyprotein
A, B
114Mason-Pfizer monkey virusMutation(s): 1 
Gene Names: gag-pro-pol
EC: 3.6.1.23 (PDB Primary Data), 3.4.23 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
Find proteins for P07572 (Mason-Pfizer monkey virus)
Go to UniProtKB:  P07572
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PRO-0A1-VAL-PSA-ALA-MET-THR
I
7synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
0A1
Query on 0A1
I
L-PEPTIDE LINKINGC10 H13 N O3TYR
PSA
Query on PSA
I
PEPTIDE-LIKEC11 H15 N O3PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.947α = 90
b = 29.504β = 101.71
c = 85.39γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Academy of SciencesCzech RepublicRVO 61388963

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release