Crystal structure of the Herpes Simplex virus type 1 DNA polymerase

Experimental Data Snapshot

  • Resolution: 2.68 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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Crystal structure of the herpes simplex virus 1 DNA polymerase.

Liu, S.Knafels, J.D.Chang, J.S.Waszak, G.A.Baldwin, E.T.Deibel, M.R.Thomsen, D.R.Homa, F.L.Wells, P.A.Tory, M.C.Poorman, R.A.Gao, H.Qiu, X.Seddon, A.P.

(2006) J Biol Chem 281: 18193-18200

  • DOI: https://doi.org/10.1074/jbc.M602414200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Herpesviruses are the second leading cause of human viral diseases. Herpes Simplex Virus types 1 and 2 and Varicella-zoster virus produce neurotropic infections such as cutaneous and genital herpes, chickenpox, and shingles. Infections of a lymphotropic nature are caused by cytomegalovirus, HSV-6, HSV-7, and Epstein-Barr virus producing lymphoma, carcinoma, and congenital abnormalities. Yet another series of serious health problems are posed by infections in immunocompromised individuals. Common therapies for herpes viral infections employ nucleoside analogs, such as Acyclovir, and target the viral DNA polymerase, essential for viral DNA replication. Although clinically useful, this class of drugs exhibits a narrow antiviral spectrum, and resistance to these agents is an emerging problem for disease management. A better understanding of herpes virus replication will help the development of new safe and effective broad spectrum anti-herpetic drugs that fill an unmet need. Here, we present the first crystal structure of a herpesvirus polymerase, the Herpes Simplex Virus type 1 DNA polymerase, at 2.7 A resolution. The structural similarity of this polymerase to other alpha polymerases has allowed us to construct high confidence models of a replication complex of the polymerase and of Acyclovir as a DNA chain terminator. We propose a novel inhibition mechanism in which a representative of a series of non-nucleosidic viral polymerase inhibitors, the 4-oxo-dihydroquinolines, binds at the polymerase active site interacting non-covalently with both the polymerase and the DNA duplex.

  • Organizational Affiliation

    Exploratory Medicinal Sciences, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA. shenping.liu@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase
A, B
1,193Human alphaherpesvirus 1 strain KOSMutation(s): 0 
Gene Names: UL30
Find proteins for P04292 (Human herpesvirus 1 (strain KOS))
Explore P04292 
Go to UniProtKB:  P04292
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04292
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.68 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.917α = 90
b = 125.55β = 90
c = 220.577γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2006-05-16 
  • Deposition Author(s): Liu, S.

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description