6EY7

Human cytomegalovirus terminase nuclease domain, Mn soaked, inhibitor bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Driven Discovery of alpha , gamma-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase.

Bongarzone, S.Nadal, M.Kaczmarska, Z.Machon, C.Alvarez, M.Albericio, F.Coll, M.

(2018) ACS Omega 3: 8497-8505

  • DOI: 10.1021/acsomega.8b01472
  • Primary Citation of Related Structures:  
    6EY7

  • PubMed Abstract: 
  • Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymeras ...

    Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymerase inhibitors have several drawbacks. An alternative strategy is to use compounds against the packaging machinery or terminase complex, which is essential for viral replication. Our discovery that raltegravir ( 1 ), a human immunodeficiency virus drug, inhibits the nuclease function of UL89, one of the protein subunits of the complex, prompted us to further develop terminase inhibitors. On the basis of the structure of 1 , a library of diketoacid (α,γ-DKA and β,δ-DKA) derivatives were synthesized and tested for UL89-C nuclease activity. The mode of action of α,γ-DKA derivatives on the UL89 active site was elucidated by using X-ray crystallography, molecular docking, and in vitro experiments. Our studies identified α,γ-DKA derivative 14 able to inhibit UL89 in vitro in the low micromolar range, making 14 an optimal candidate for further development and virus-infected cell assay.


    Organizational Affiliation

    Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UL89 HCMV terminaseABCD279Human herpesvirus 5 strain AD169Mutation(s): 0 
Gene Names: UL89TRM3
EC: 3.1
Find proteins for P16732 (Human cytomegalovirus (strain AD169))
Explore P16732 
Go to UniProtKB:  P16732
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.65α = 90
b = 87.65β = 90
c = 186.58γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and CompetitivenessSpainBFU2011-22588
Ministry of Economy and CompetitivenessSpainCTQ2012-30930
Ministry of Economy and CompetitivenessSpainCTQ2015-67870P
Ministry of Economy and CompetitivenessSpainBFU2014-53550-P
European UnionBelgiumSILVER-GA 260644

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-09-11
    Changes: Data collection, Database references