1P73

Crystal structure of EHV4-TK complexed with TP4A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis for the dual thymidine and thymidylate kinase activity of herpes thymidine kinases.

Gardberg, A.Shuvalova, L.Monnerjahn, C.Konrad, M.Lavie, A.

(2003) Structure 11: 1265-1277

  • DOI: 10.1016/j.str.2003.09.003
  • Primary Citation of Related Structures:  
    1P6X, 1P72, 1P73, 1P75, 1P7C

  • PubMed Abstract: 
  • Crystal structures of equine herpesvirus type-4 thymidine kinase (EHV4-TK) in complex with (i). thymidine and ADP, (ii). thymidine and SO(4) and the bisubstrate analogs, (iii). TP(4)A, and (iv). TP(5)A have been solved. Additionally, the structure of herpes simplex virus type-1 thymidine kinase (HSV1-TK) in complex with TP(5)A has been determined ...

    Crystal structures of equine herpesvirus type-4 thymidine kinase (EHV4-TK) in complex with (i). thymidine and ADP, (ii). thymidine and SO(4) and the bisubstrate analogs, (iii). TP(4)A, and (iv). TP(5)A have been solved. Additionally, the structure of herpes simplex virus type-1 thymidine kinase (HSV1-TK) in complex with TP(5)A has been determined. These are the first structures of nucleoside kinases revealing conformational transitions upon binding of bisubstrate analogs. The structural basis for the dual thymidine and thymidylate kinase activity of these TKs is elucidated. While the active sites of HSV1-TK and EHV4-TK resemble one another, notable differences are observed in the Lid regions and in the way the enzymes bind the base of the phosphoryl-acceptor. The latter difference could partly explain the higher activity of EHV4-TK toward the prodrug ganciclovir.


    Organizational Affiliation

    University of Illinois at Chicago, Department of Biochemistry and Molecular Biology, 1819 West Polk St, Chicago, IL 60612, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidine kinaseA, B, C, D334Equid alphaherpesvirus 4Mutation(s): 0 
Gene Names: TK
EC: 2.7.1.21
UniProt
Find proteins for P24425 (Equine herpesvirus 4 (strain 1942))
Explore P24425 
Go to UniProtKB:  P24425
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4TA (Subject of Investigation/LOI)
Query on 4TA

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], Q [auth C], S [auth D]P1-(5'-ADENOSYL)P4-(5'-(2'-DEOXY-THYMIDYL))TETRAPHOSPHATE
C20 H25 N7 O20 P4
WLGHSSFVEUABFP-SLFMBYJQSA-J
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , 
E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.347α = 90
b = 118.293β = 90
c = 122.652γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance