1JQ7

HCMV protease dimer-interface mutant, S225Y complexed to Inhibitor BILC 408


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease.

Batra, R.Khayat, R.Tong, L.

(2001) Nat.Struct.Mol.Biol. 8: 810-817

  • DOI: 10.1038/nsb0901-810
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Biochemical studies indicate that dimerization is required for the catalytic activity of herpesvirus proteases, whereas structural studies show a complete active site in each monomer, away from the dimer interface. Here we report kinetic, biophysical ...

    Biochemical studies indicate that dimerization is required for the catalytic activity of herpesvirus proteases, whereas structural studies show a complete active site in each monomer, away from the dimer interface. Here we report kinetic, biophysical and crystallographic characterizations of structure-based mutants in the dimer interface of human cytomegalovirus (HCMV) protease. Such mutations can produce a 1,700-fold reduction in the kcat while having minimal effects on the K(m). Dimer stability is not affected by these mutations, suggesting that dimerization itself is insufficient for activity. There are large changes in monomer conformation and dimer organization of the apo S225Y mutant enzyme. However, binding of an activated peptidomimetic inhibitor induced a conformation remarkably similar to the wild type protease. Our studies suggest that appropriate dimer formation may be required to indirectly stabilize the protease oxyanion hole, revealing a novel mechanism for dimerization to regulate enzyme activity.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASSEMBLIN
A, B
256Human cytomegalovirus (strain AD169)Mutation(s): 2 
Gene Names: UL80 (APNG)
Find proteins for P16753 (Human cytomegalovirus (strain AD169))
Go to UniProtKB:  P16753
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0FP
Query on 0FP

Download SDF File 
Download CCD File 
A, B
N-(6-aminohexanoyl)-3-methyl-L-valyl-3-methyl-L-valyl-N~1~-[(2S,3S)-3-hydroxy-4-oxo-4-{[(1R)-1-phenylpropyl]amino}butan-2-yl]-N~4~,N~4~-dimethyl-L-aspartamide
BILC 408
C37 H63 N7 O7
RICYNZHPHSJRNO-GYZAPQSVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.260 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.250α = 90.00
b = 74.250β = 90.00
c = 215.800γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
COMOphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other