3MJR

Human dCK complex with Acyclic Nucleoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 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
  • Primary Citation of Related Structures:  
    3MJR

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidine kinaseA, B, C, D279Homo sapiensMutation(s): 0 
Gene Names: DCK
EC: 2.7.1.74 (PDB Primary Data), 2.7.1.76 (UniProt), 2.7.1.113 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens)
Explore P27707 
Go to UniProtKB:  P27707
PHAROS:  P27707
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.258 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.31α = 90
b = 97.31β = 90
c = 121.5γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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