1UEI

Crystal structure of human uridine-cytidine kinase 2 complexed with a feedback-inhibitor, UTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase

Suzuki, N.N.Koizumi, K.Fukushima, M.Matsuda, A.Inagaki, F.

(2004) STRUCTURE 12: 751-764

  • DOI: 10.1016/j.str.2004.02.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uridine-cytidine kinase (UCK) catalyzes the phosphorylation of uridine and cytidine and activates pharmacological ribonucleoside analogs. Here we present the crystal structures of human UCK alone and in complexes with a substrate, cytidine, a feedbac ...

    Uridine-cytidine kinase (UCK) catalyzes the phosphorylation of uridine and cytidine and activates pharmacological ribonucleoside analogs. Here we present the crystal structures of human UCK alone and in complexes with a substrate, cytidine, a feedback inhibitor, CTP or UTP, and with phosphorylation products, CMP and ADP, respectively. Free UCK takes an alpha/beta mononucleotide binding fold and exists as a homotetramer with 222 symmetry. Upon inhibitor binding, one loop region was loosened, causing the UCK tetramer to be distorted. Upon cytidine binding, a large induced fit was observed at the uridine/cytidine binding site, which endows UCK with a strict specificity for pyrimidine ribonucleosides. The first UCK structure provided the structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase, which give clues for the design of novel antitumor and antiviral ribonucleoside analogs that inhibit RNA synthesis.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of human uridine-cytidine kinase 2
      Suzuki, N.N.,Koizumi, K.,Fukushima, M.,Matsuda, A.,Inagaki, F.
      (2003) ACTA CRYSTALLOGR.,SECT.D 59: 1477


    Organizational Affiliation

    Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N12 W6 Kita-ku, Sapporo 060-0812, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine-cytidine kinase 2
A, B
252Homo sapiensMutation(s): 0 
Gene Names: UCK2 (UMPK)
EC: 2.7.1.48
Find proteins for Q9BZX2 (Homo sapiens)
Go to Gene View: UCK2
Go to UniProtKB:  Q9BZX2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UTP
Query on UTP

Download SDF File 
Download CCD File 
A, B
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 131.529α = 90.00
b = 247.748β = 90.00
c = 91.673γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CrystalCleardata scaling
CNSrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance