1UEJ

Crystal structure of human uridine-cytidine kinase 2 complexed with a substrate, cytidine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.213 

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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT
Download SDF File 
Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
CTN
Query on CTN
Download SDF File 
Download CCD File 
A, B
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
CYTIDINE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.213 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 138.296α = 90.00
b = 247.631β = 90.00
c = 90.944γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

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