6LYV

The crystal structure of SAUGI/KSHVUDG complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report



Literature

Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases.

Liao, Y.T.Lin, S.J.Ko, T.P.Liu, C.Y.Hsu, K.C.Wang, H.C.

(2020) Int J Biol Macromol 160: 903-914

  • DOI: 10.1016/j.ijbiomac.2020.05.267
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Uracil-DNA glycosylases (UDGs) are conserved DNA-repair enzymes that can be found in many species, including herpesviruses. Since they play crucial roles for efficient viral DNA replication in herpesviruses, they have been considered as potential ant ...

    Uracil-DNA glycosylases (UDGs) are conserved DNA-repair enzymes that can be found in many species, including herpesviruses. Since they play crucial roles for efficient viral DNA replication in herpesviruses, they have been considered as potential antiviral targets. In our previous work, Staphylococcus aureus SAUGI was identified as a DNA mimic protein that targets UDGs from S. aureus, human, Herpes simplex virus (HSV) and Epstein-Barr virus (EBV). Interestingly, SAUGI has the strongest inhibitory effects with EBVUDG. Here, we determined complex structures of SAUGI with EBVUDG and another γ-herpesvirus UDG from Kaposi's sarcoma-associated herpesvirus (KSHVUDG), which SAUGI fails to effectively inhibit. Structural analysis of the SAUGI/EBVUDG complex suggests that the additional interaction between SAUGI and the leucine loop may explain why SAUGI shows the highest binding capacity with EBVUDG. In contrast, SAUGI appears to make only partial contacts with the key components responsible for the compression and stabilization of the DNA backbone in the leucine loop extension of KSHVUDG. The findings in this study provide a molecular explanation for the differential inhibitory effects and binding strengths that SAUGI has on these two UDGs, and the structural basis of the differences should be helpful in developing inhibitors that would interfere with viral DNA replication.


    Organizational Affiliation

    The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan. Electronic address: wanghc@tmu.edu.tw.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uracil-DNA glycosylase
A, C, E, G, I, K, M, O
255Human gammaherpesvirus 8Mutation(s): 0 
Gene Names: ORF46HHV8GK18_gp50
EC: 3.2.2.27
Find proteins for Q76RG8 (Human herpesvirus 8)
Go to UniProtKB:  Q76RG8

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SAUGI
B, D, F, H, J, L, N, P
112Staphylococcus aureusMutation(s): 0 
Find proteins for Q936H5 (Staphylococcus aureus)
Go to UniProtKB:  Q936H5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.887α = 108.141
b = 92.196β = 90.612
c = 98.107γ = 92.229
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan103-2311-B-038-005-MY3
Ministry of Science and Technology (MoST, Taiwan)Taiwan106-2311-B-038-002
Ministry of Science and Technology (MoST, Taiwan)Taiwan106-2313-B-038 -004 -MY3

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release