4XSD

Complex structure of thymidylate synthase from varicella zoster virus with a dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Varicella Zoster Virus Thymidylate Synthase Establishes Functional and Structural Similarities as the Human Enzyme and Potentiates Itself as a Target of Brivudine.

Hew, K.Dahlroth, S.L.Veerappan, S.Pan, L.X.Cornvik, T.Nordlund, P.

(2015) PLoS One 10: e0143947-e0143947

  • DOI: https://doi.org/10.1371/journal.pone.0143947
  • Primary Citation of Related Structures:  
    4XSC, 4XSD, 4XSE

  • PubMed Abstract: 

    Varicella zoster virus (VZV) is a highly infectious human herpesvirus that is the causative agent for chicken pox and shingles. VZV encodes a functional thymidylate synthase (TS), which is the sole enzyme that produces dTMP from dUMP de novo. To study substrate binding, the complex structure of TSVZV with dUMP was determined to a resolution of 2.9 Å. In the absence of a folate co-substrate, dUMP binds in the conserved TS active site and is coordinated similarly as in the human encoded TS (TSHS) in an open conformation. The interactions between TSVZV with dUMP and a cofactor analog, raltitrexed, were also studied using differential scanning fluorimetry (DSF), suggesting that TSVZV binds dUMP and raltitrexed in a sequential binding mode like other TS. The DSF also revealed interactions between TSVZV and in vitro phosphorylated brivudine (BVDUP), a highly potent anti-herpesvirus drug against VZV infections. The binding of BVDUP to TSVZV was further confirmed by the complex structure of TSVZV and BVDUP solved at a resolution of 2.9 Å. BVDUP binds similarly as dUMP in the TSHS but it induces a closed conformation of the active site. The structure supports that the 5-bromovinyl substituent on BVDUP is likely to inhibit TSVZV by preventing the transfer of a methylene group from its cofactor and the subsequent formation of dTMP. The interactions between TSVZV and BVDUP are consistent with that TSVZV is indeed a target of brivudine in vivo. The work also provided the structural basis for rational design of more specific TSVZV inhibitors.


  • Organizational Affiliation

    Division of Structural Biology and Biochemistry, Nanyang Technological University, School of Biological Sciences, Singapore, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B, C, D
311Human herpesvirus 3 strain Oka vaccineMutation(s): 0 
Gene Names: ORF13
EC: 2.1.1.45
UniProt
Find proteins for Q4JQW2 (Varicella-zoster virus (strain Oka vaccine))
Explore Q4JQW2 
Go to UniProtKB:  Q4JQW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4JQW2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.17α = 90
b = 150.17β = 90
c = 89.16γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2015-12-16 
  • Deposition Author(s): Hew, K.

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description