2A30

Crystal structure of human deoxycytidine kinase in complex with deoxycytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the preference of UTP over ATP in human deoxycytidine kinase: illuminating the role of main-chain reorganization.

Godsey, M.H.Ort, S.Sabini, E.Konrad, M.Lavie, A.

(2006) Biochemistry 45: 452-461

  • DOI: 10.1021/bi0518646
  • Primary Citation of Related Structures:  2A2Z

  • PubMed Abstract: 
  • Human deoxycytidine kinase (dCK) uses nucleoside triphosphates to phosphorylate several clinically important prodrugs in addition to its natural substrates. Although UTP is the preferred phosphoryl donor for this reaction, our previous studies report ...

    Human deoxycytidine kinase (dCK) uses nucleoside triphosphates to phosphorylate several clinically important prodrugs in addition to its natural substrates. Although UTP is the preferred phosphoryl donor for this reaction, our previous studies reported dCK structures solely containing ADP in the phosphoryl donor binding site. To determine the molecular basis of the kinetically observed phosphoryl donor preference, we solved crystal structures of a dCK variant lacking a flexible insert (residues 65-79) but having similar catalytic properties as wild type, in complex with deoxycytidine (dC) and UDP, and in the presence of dC but the absence of UDP or ADP. These structures reveal major changes in the donor base binding loop (residues 240-247) between the UDP-bound and ADP-bound forms, involving significant main-chain rearrangement. This loop is disordered in the dCK-dC structure, which lacks a ligand at the phosphoryl donor site. In comparison with the ADP-bound form, in the presence of UDP this loop is shifted inward to make closer contact to the smaller uracil base. These structures illuminate the phosphoryl donor binding and preference mechanisms of dCK.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 South Ashland Avenue, Chicago, Illinois 60607, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidine kinase
A, B, C, D
248Homo sapiensGene 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
DCZ
Query on DCZ

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYCYTIDINE
C9 H13 N3 O4
CKTSBUTUHBMZGZ-SHYZEUOFSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.337α = 90.00
b = 64.941β = 95.97
c = 108.602γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
XSCALEdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance