3QEO

S74E-R104M-D133A dCK variant in complex with L-deoxythymidine and UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release.

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

(2011) Biochemistry 50: 2870-2880

  • DOI: 10.1021/bi2001032
  • Primary Citation of Related Structures:  
    3QEJ, 3QEN, 3QEO

  • PubMed Abstract: 
  • Deoxycytidine kinase (dCK) uses either ATP or UTP as a phosphoryl donor to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is distant from the active site ...

    Deoxycytidine kinase (dCK) uses either ATP or UTP as a phosphoryl donor to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is distant from the active site. Replacing the serine with a glutamic acid (S74E variant) can mimic phosphorylation of Ser74. To understand how phosphorylation affects the catalytic properties of dCK, we examined the S74E variant of dCK both structurally and kinetically. We observe that the presence of a glutamic acid at position 74 favors the adoption by the enzyme of the open conformation. Glu74 stabilizes the open conformation by directly interacting with the indole side chain of Trp58, a residue that is in the proximity of the base of the nucleoside substrate. The open dCK conformation is competent for the binding of nucleoside but not for phosphoryl transfer. In contrast, the closed conformation is competent for phosphoryl transfer but not for product release. Thus, dCK must make the transition between the open and closed states during the catalytic cycle. We propose a reaction scheme for dCK that incorporates the transition between the open and closed states, and this serves to rationalize the observed kinetic differences between wild-type dCK and the S74E variant.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxycytidine kinaseA, B279Homo sapiensMutation(s): 7 
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
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
LLT (Subject of Investigation/LOI)
Query on LLT

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]L-deoxythymidine
C10 H14 N2 O5
IQFYYKKMVGJFEH-CSMHCCOUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.200 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.76α = 90
b = 68.76β = 90
c = 120.597γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2011-01-20 
  • Released Date: 2011-03-16 
  • Deposition Author(s): Lavie, A., Hazra, S.

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance