3MJR

Human dCK complex with Acyclic Nucleoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Sugar Ring of the Nucleoside Is Required for Productive Substrate Positioning in the Active Site of Human Deoxycytidine Kinase (dCK): Implications for the Development of dCK-Activated Acyclic Guanine Analogues.

Hazra, S.Konrad, M.Lavie, A.

(2010) J.Med.Chem. 53: 5792-5800

  • DOI: 10.1021/jm1005379

  • PubMed Abstract: 
  • The low toxicity of acyclovir (ACV) is mainly due to the fact that human nucleoside kinases have undetectable phosphorylation rates with this acyclic guanine analogue. In contrast, herpes virus thymidine kinase (HSV1-TK) readily activates ACV. We wan ...

    The low toxicity of acyclovir (ACV) is mainly due to the fact that human nucleoside kinases have undetectable phosphorylation rates with this acyclic guanine analogue. In contrast, herpes virus thymidine kinase (HSV1-TK) readily activates ACV. We wanted to understand why human deoxycytidine kinase (dCK), which is related to HSV1-TK and phosphorylates deoxyguanosine, does not accept acyclic guanine analogues as substrates. Therefore, we crystallized dCK in complex with ACV at the nucleoside phosphoryl acceptor site and UDP at the phosphoryl donor site. The structure reveals that while ACV does bind at the dCK active site, it does so adopting a nonproductive conformation. Despite binding ACV, the enzyme remains in the open, inactive state. In comparison to ACV binding to HSV1-TK, in dCK, the nucleoside base adopts a different orientation related by about a 60 degrees rotation. Our analysis suggests that dCK would phosphorylate acyclic guanine analogues if they can induce a similar rotation.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics University of Illinois at Chicago, Chicago, Illinois 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidine kinase
A, B, C, D
279Homo sapiensMutation(s): 0 
Gene Names: DCK
EC: 2.7.1.74
Find proteins for P27707 (Homo sapiens)
Go to Gene View: DCK
Go to UniProtKB:  P27707
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B, C, D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
AC2
Query on AC2

Download SDF File 
Download CCD File 
A, B, D
9-HYROXYETHOXYMETHYLGUANINE
C8 H11 N5 O3
MKUXAQIIEYXACX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.258 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 97.310α = 90.00
b = 97.310β = 90.00
c = 121.500γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
MOLREPphasing
XDSdata scaling
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-04-13 
  • Released Date: 2010-07-28 
  • Deposition Author(s): Hazra, S., Lavie, A.

Revision History 

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description