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 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


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:  
    1UDW, 1UEJ, 1UEI, 1UFQ, 1UJ2

  • 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 feedback inhibitor, CTP or UTP, and with phosphorylation products, CMP and ADP, respectively ...

    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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uridine-cytidine kinase 2A, B252Homo sapiensMutation(s): 0 
Gene Names: UCK2UMPK
EC: 2.7.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZX2 (Homo sapiens)
Explore Q9BZX2 
Go to UniProtKB:  Q9BZX2
PHAROS:  Q9BZX2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTN (Subject of Investigation/LOI)
Query on CTN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-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 
  • R-Value Observed: 0.213 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.296α = 90
b = 247.631β = 90
c = 90.944γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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