2BT1 | pdb_00002bt1

Epstein Barr Virus dUTPase in complex with a,b-imino dUTP

• PDB DOI: https://doi.org/10.2210/pdb2BT1/pdb

• Classification: HYDROLASE
• Organism(s): human gammaherpesvirus 4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-24 Released: 2005-09-15 
• Deposition Author(s): Tarbouriech, N., Buisson, M., Seigneurin, J.-M., Cusack, S., Burmeister, W.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

The Monomeric Dutpase from Epstein-Barr Virus Mimics Trimeric Dutpases

Tarbouriech, N., Buisson, M., Seigneurin, J.-M., Cusack, S., Burmeister, W.P.

(2005) Structure 13: 1299

• PubMed: 16154087 
• DOI: https://doi.org/10.1016/j.str.2005.06.009
• Primary Citation Related Structures: 
  2BSY, 2BT1


• PubMed Abstract: 
  

  Deoxyuridine 5'-triphosphate pyrophosphatases (dUTPases) are ubiquitous enzymes cleaving dUTP into dUMP and pyrophosphate. They occur as monomeric, dimeric, or trimeric molecules. The trimeric and monomeric enzymes both contain the same five characteristic sequence motifs but in a different order, whereas the dimeric enzymes are not homologous. Monomeric dUTPases only occur in herpesviruses, such as Epstein-Barr virus (EBV). Here, we describe the crystal structures of EBV dUTPase in complex with the product dUMP and a substrate analog alpha,beta-imino-dUTP. The molecule consists of three domains forming one active site that has a structure extremely similar to one of the three active sites of trimeric dUTPases. The three domains functionally correspond to the subunits of the trimeric form. Domains I and II have the dUTPase fold, but they differ considerably in the regions that are not involved in the formation of the unique active site, whereas domain III has only little secondary structure.

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Organizational Affiliation: 
• EMBL-Grenoble Outstation, BP181, F-38042 Grenoble cedex 9, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 31.49 kDa 
• Atom Count: 2,100 
• Modeled Residue Count: 254 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE	A	278	human gammaherpesvirus 4	Mutation(s): 0  EC: 3.6.1.23
UniProt
Find proteins for P03195 (Epstein-Barr virus (strain B95-8)) Explore P03195  Go to UniProtKB:  P03195

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DUP	B [auth A]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C9 H16 N3 O13 P3 XZLLMTSKYYYJLH-SHYZEUOFSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.585	α = 90
b = 146.585	β = 90
c = 77.145	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-15 
Deposition Author(s): Tarbouriech, N., Buisson, M., Seigneurin, J.-M., Cusack, S., Burmeister, W.P.

Revision History  

• Version 1.0: 2005-09-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary